Engine Removal and Transmission Repair FAQ  (1st Draft)
by Flash #412
slightly edited & some extra photos added by Kristian #562
12/09/02

• Removing the Motor from an F650 Classic

• Splitting the Cases of an F650 Classic
• Reinstalling the Motor into an F650 Classic
• Difficulty getting the Cases Back Together
• See also Flash's Notes when you do the Gear Change Work
• Additional Notes for Clutch Nut Removal if Required
• Can I remove the alternator after pulling the motor
• See also the Timing Flywheel FAQ for why it won't start after it has been put back together.
• For Oil Pump Gears

Removing the Motor from an F650 Classic

The idea of this FAQ is to explain how to remove the motor from an F650 with the intention of disassembling it further. Some of the disassembly is easier with the motor in the frame, making the motor lighter and easier to remove from the frame. If that is not your intent, you should probably think real hard about which steps to skip.

Useful Tools:

• Clutch Holder Pliers
• Propane Torch
• TDC Bolt
• 13mm Box End Wrench (Open Ended Spanner)
• 2 x 22mm Sockets, 26mm, 30mm Socket/Wrench
• Impact Wrench
• A pair of 14mm bolts at least 100mm long, the less thread, the better.
• Tie-Wraps
• BMW Special Flywheel Puller Tool (You can buy Cartool #12-5-510)

I like to start with a box of gallon size zip-lock bags and a box of zip-lock sandwich bags. I put complete sub-assemblies in a single bag. One bag of screws looks pretty much like another so if there is any possibility of doubt, I use a Sharpie to note the contents on the outside of the bag.

Clicking on any of the picture opens them up a lot BIGGER.

1. Park it on the center stand.

2. Remove the seat.

3. Remove the left side cover (covering the battery) and remove the battery. Remove the right side cover, too. Refer the Battery FAQ for Battery Removal Tips

4. Remove the black engine covers from both sides and the black plastic radiator piece.

5. Remove the gas tank. Refer the Gas Tank Removal-Replacement FAQ.
   
    

6. Remove the windshield and then the fairing. Refer the Fairing FAQ. (Tip: when the windshield is off after removing the tank and the rest of the plastic, you need only remove the two screws above the headlight facing RIGHT and LEFT, not the two facing front.)  Unplug the turn signal connections by simply pulling. Unplug the H-4 headlight connector. Pull the parking light out of the reflector assembly.

7. Remove the plastic "bash plate" from below the motor.

8. Drain the oil from the sump and the oil tank (bolt on frame down tube). Refer the Oil Change FAQ.
   
   

9. Drain the coolant using the bottom bolt on the water pump. Refer the Coolant Change FAQ.
   
   

10. Remove the clamps from the radiator hoses, pull the hoses off and remove the radiator bolts. Cut the tie wrap at the fan wiring and unplug the fan connector. Pull the temperature sensor wire from the motor at the same time. Remove the radiator, with the fan remaining installed.
    
    
     

11. On the right side of the motor, remove the counter shaft cover and the little two-screw electric cover at the cylinder base. Remove all the the hoses over there. (If you haven't taken your bike apart before, take all the cheap, original equipment hose clamps to a cheapo car parts place and buy some REAL hose clamps with which to replace them.)
    
    

12. Knock the countershaft sprocket lock washer back flat(ish) with a hammer & screwdriver and loosen the nut that holds the sprocket (30mm socket). You want to do this with the engine in the frame so you can put the bike in gear and/or step on the brake as needed. Do NOT remove the sprocket yet. You will need the brake to hold the input shaft while you loosen the nut from the clutch basket.
    
    

13. Remove the top motor mount completely from the frame and the motor.
    
    

14. Remove the bolt that holds the shock adjuster. Let the adjuster dangle. You'll need to move it here and there to get it out of your way while doing various things. Generally, use a bungee to keep it held in place.

15. Totally loosen the hose clamps on the intake manifold and the airbox. Wiggle the carb set to break the grip the rubber has on the carbs. A shot of Son of a Gun or Armor-All or even WD-40 will assist greatly. Wiggle the carb set loose and pull them out the top. Stop and pull the vacuum hoses off the right side carb. Actually, you only need to pull ONE hose off (the forward one) if you have done the Canisterectomy already. The other (rearward one) should just be a nub with a plugged end. Refer Carbs Out for more Details on Carb Removal.
    
    

16. Reinstall the top motor mount. (You don't need to torque anything. But this is the LAST mount to be removed when everything else is done.)

17. Unhook both spark plug wires and remove ONE spark plug (either one).
    
    

18. With an open end wrench, loosen both ends of the air injector pipe. One end connects to a fitting on the bottom of the air box and the other to the exhaust header.  You'll need to remove the screw from the area above the right footpeg that holds the retaining clip that retains this pipe before you can remove this pipe. It takes some wiggling and turning, but it can be removed and reinstalled with the exhaust system in place.

19. With a 13mm box end wrench, remove the four nuts that hold the clamps that hold the header pipes in place. Loosen the Allen head bolt on the clamp where the "u-pipe" header piece goes into the collector piece. Loosen the Allen bolt on the clamp where the collector goes into the muffler. Wiggle stuff and remove both headers and the collector. You can leave the muffler undisturbed.
    
    

20. Operate on the footpegs by removing the forward nut & bolt from each footpeg and just loosening the other to allow you to pivot the footpegs back out of the way.  (Or remove them entirely, your choice.)

21. On the left side of the motor, remove the electric cable from the starter and both starter bolts and remove the starter. It just pulls out with some wiggling after the bolts are out. Stick the bolts back into their holes. They'll give something to pull on to remove the cover when you get to it.

22. Remove whatever hoses you see around there that need removing. By the way, throw ALL the damned BMW single-use cheap-crap hose clamps away after you measure them so you can replace them with REAL hose clamps.

23. Remove the two bolts that bolt the down-tube frame piece to the motor (and crash bars if installed) and the two bolts that secure it to the actual frame. (The rear part of the subframe was held with the footpeg nuts & bolts.)  Remove this frame piece, along with the side stand (and crash bars if installed). You can leave the metal "hose piece" up at the front hanging.
    
    

24. Pull the clutch lever in at the handlebar with one hand and grab the cable with the other hand, near the bottom end. When you release the clutch lever, pull hard on the cable sheath. You can quickly and easily remove it from the boss this way. Then pull the end of the clutch cable out of the lower clutch fork.
    
    

25. Remove the bolt from the shift lever and then remove the shift lever.
    
    

26. While you're over there, crack the cam chain tensioner bolt loose, but do not remove it. It is that bolt halfway between the crankcase and the head on the back side of the cylinder. You'll need a 22mm wrench.
    
    

27. Remove all the bolts holding the left side engine (clutch) cover and remove the cover. The bike is going to pee some more oil and possibly water when you do this. So you should probably be prepared with a big drain pan and maybe some newspaper. Hey look!  It's the clutch!  (Try not to tear the paper gasket.)
    
     

27. Remove all six bolts. Do this by "cracking" all six of them a half turn or so and then just removing every other bolt. Take each of the last three bolts and give them about two turns at a time until all six bolts are out. Remove the clutch pack. PAY ATTENTION to how it comes out so you can put it back in the same way (with a metal disk going in last).
    
    

28. Flatten the tab washer and then use a 1-1/16" or 26 mm socket (and the rear brake with the trans in gear) to loosen the nut holding the clutch basket. Then remove the nut. Behind the nut is a splined washer. This may be difficult to remove because it may have rotated. Take a dental pick or something similar and rotate it to line up the splines and then get behind it and pop it off. An O-ring is supposed to be behind it on the shaft. You may have problems removing this Nut, so try inserting the TDC Bolt, use HEAT on the Nut, a long BREAKER BAR and your or someone's foot on the BRAKE (You will need the the bike in Gear for this to work). If you still have problems removing this Nut, See Additional Notes for Clutch Nut Removal if Required.

29. Here is the trick to removing the basket... put the clutch pressure plate cover back on without any plates. Stick three screws back in SIX TURNS EACH in every-other hole with the washers but without the springs. Push the cover in and then YANK it out. When it hits the bolt heads, the basket pops off. If not, go again. The included picture was actually taken just before doing this.
    
    

30. Loosen the nut at the top of the tachometer drive on the motor near the clutch shaft and pull out the Tach drive cable. You can then pull off the plastic Tach-drive gears.

31. Either stick a big Allen wrench in the end of the crank sticking through the alternator or put a 30mm wrench on the nut on the end of the crank on the left side (as pictured) and put your finger over the empty spark plug hole. Crank the motor over (turning clockwise viewed from the right side, counter clockwise viewed from the left), until you feel it start coming up on compression. Stick a long, thin screwdriver (or other probe) down the plug hole and slowly crank the engine over, making sure that the "probe" is able to rise freely as the motor turns over. When the probe stops rising and then starts falling, reverse direction until you find Top Dead Center (or thereabouts). Remove the bolt on the left side of the motor where the crank-stop bolt goes. Turn the crank stop bolt (blue t-handle tool is in it in the picture) in while rocking the crank back and forth in the vicinity of TDC until you feel the crank stop bolt go into the slot in the crank. Take a look at the picture of the inside the split crankcase (below left, taken much later in this process) for some clarification of how the crank stop bolt works to stop the crank. The thumb points to the bolt in the red circle and the forefinger points to the slot in the crank in the green oval.
    
              OR

32. Use a 30mm wrench or socket to remove the nut from the crank timing sprocket. Pull the lock washer loose. The sprocket will just pull off once the timing chain is loose. There is no need to remove the woodruff key from the crankshaft.

33. There is no need to remove the two identical black plastic gears from the oil pumps (unless you have a reason. If you do need to remove them pry them off. They just POP onto a pin that is across the pump shaft.
    
    

34. Back around the right side of the bike... If you have a clip-type master link, pull it and remove the chain. If not, loosen the rear axle and push the rear wheel all the way forward so you can roll the chain off the rear sprocket. Then remove the chain from the front sprocket. Remove the nut and lock-washer and pull off the sprocket. Refer the Chain Sprockets FAQ.

35. Remove the oil filter cover and filter.
    
    

36. Trace the wires from the right side engine (alternator) cover and the oil pressure sensor up to where they go in the vicinity of where the battery lives and unplug all of them. You don't need to pay attention to which wire goes where because they used a different connector for each wire so you can't mess up when you put it back together.

37. Remove all the bolts that hold the right side engine (alternator) cover. Pull the cover off. It does not want to come off even when all the bolts are out because there is a big honking magnet in there. Might be good to take your (mechanical wristwatch) off before you do this. The trigger wires should stay with the trigger. The rest of the wires go with the cover or else get "removed" or tucked out of the way.
    
     

38. If you don't intend to split the cases, you don't need to pull the alternator. Otherwise, remove the nut from the alternator rotor. Then use the BMW special alternator puller tool (BMW part number XX-XXX?  Cartool 12-5-510, costs about US$24 or so). This puller tool that has internal thread of 37 or 38 mm with a pitch of 1.5 mm also fits a significant percentage of dirt bikes now on the market.
    

39. After the alternator rotor is out, remove the starter gears and spacers. The reason you are pulling the alternator is so that you can get to the case screws behind the starter gears (circled in yellow in the case photo).
    
    

40. If there are any other hoses or wires, remove one end or the other until the only thing between the engine and the frame are the mounting bolts.

41. Because the bottom of the motor is not flat, a jig helps with the un-installation and disassembly. A dimensioned drawing of the jig I made is linked. This thing is not perfect, but works. An improvement would be bolting a couple of pieces of metal to the front-most piece of wood so that the thing could be bolted to the lower front engine mount. After pulling the motor three times, I figured out the easiest way for me to do it. Perhaps it will work for you. At this point, the motor has three mounts in place, the one at the top, the swing arm bolt and the bolt below the swing arm.  

42. The bolt that goes through the motor at the top motor mount should be LOOSE. But do not remove it at this stage. This bolt comes out last.

43. Pry off the black plastic swing arm bolt covers. Use two 22 mm sockets and loosen the nut from the swing arm bolt. Remove the nut and washer. [HOMEMADE SPECIAL TOOL: Get a pair of 14mm bolts at least 100mm long, the less thread, the better. Wrap a Ty-Wrap tightly around each bolt, up near the head.]  Use one of the "special-tool" 14mm bolts to knock the swing arm bolt out. You do not want to knock this bolt in so far that it goes through the swing arm and into the motor. You want to knock it through the frame and about an inch into the swing arm. Pull the swing arm bolt out the other side and similarly install the other 14mm bolt. (These bolts significantly simplify reinstallation of the motor. If you don't have them when you pull it out, stick something in there. But try to get the bolts before you attempt to put the motor back in. Aligning the swing arm to the motor and keeping the plastic washers in place is EXTREMELY difficult without them. The Ty-Wrap near the head is just a pull tab in case the bolts get shoved in too far.)
    
       

44. Remove the engine mount bolt below the swing arm. The motor is now hanging only from the top motor mount.
    
    

45. Loosen the two bolts that hold the top motor mount to the frame. Do this fairly evenly. The motor will lower itself as you loosen these bolts and then sort of wedge itself in the frame, against hoses at the front and rear. When the motor stops, you can remove the frame-bolts and then pull the bolt that holds the motor mount to the motor. The motor is now hanging completely free, simply wedged in the frame. The photo of the jig is "upside down" so it will more closely match the drawing.

    
    
    

46. It can be removed by yourself, but is easier with assistance. Stack up some scraps of lumber under the motor, to a level a few inches below it. With your chest on the frame, you can grab both sides of the motor and pick it up, pulling the head toward the back slightly and turn it to the left, freeing it completely. And move it out toward the left side of the bike. (It is probably best not to drop it, which is why you want to pile stuff up.)  Setting it down on the jig is a good idea. Once completely free from the frame, drag the motor out from under it. Note that because of the fact you have to turn and rotate the motor to get it free from the frame, a transmission jack will NOT work to remove the motor. If the front down tube was about two or three inches shorter, life would have been MUCH simpler.
    
    

Notes:

• Take the time to inspect the rings and wrist pin retainers while you are in there - Hmmm. I did NOT want to pull the piston out. But ended up popping the bottom oil ring and then HAD to pull it to get the compressor back on. You can pull the whole jug without separating the head. The retainers are those shitty c-clips.

• How do you remove the oil pumps (2) plastic gears. They "POP" onto a pin in a cross-drilled hole in the - yet another detail that is probably not covered in the manual.

• "Remove oil pump gears." We didn't need to. But once we did, we realized that we didn't need to mess with the oil pumps since THOSE shafts didn't go anywhere. But we didn't KNOW that before we pulled the gears. You CAN leave the gears on and split the cases if you want, is what I am saying. As it was, we left the oil pumps undisturbed.

Splitting the Cases of an F650 Classic

TBA

Reinstalling the Motor into an F650 Classic

I am NOT kidding about those 14mm bolts. They will make your life SO much easier when reinstalling the motor. To put it back in... attach the top motor mount to the frame as loosely as you dare. Pick up the motor and have an assistant slip the top motor mount bolt in. THEN tighten up the frame bolts, drawing the motor upward. As you draw it up, PAY ATTENTION to how it fits between the swingarm (retained by those 14mm bolts, loosely fit in through the frame holes) and those accursed plastic washers. Once it is up, you can rock it some to get the front mounts secured. Then, you'll need to remove the top mount again, in order to do carbs and stuff. But once you've got it in the frame with the swingarm secured, the rest is just hooking stuff back up.

Difficulty getting the Cases Back Together?

Q. They keep getting hung up around the oil sender area. I wonder of I have had it a part too long. If you can remember their are 4 washers/spacers that go on (one on the CB, two at the transmission and on on the gear selector) when the cases go back together. I am enclosing a photo with the four washers circled in blue and the area that will not close in red. I tried a bit of force to close the case but the crack shaft wouldn't turn easy so I know I have a problem. I took out the washer the arrow points too and it went right together, I think that washer goes on the alternator/stator.

• All I can do is share the photo below. Figuring out what is different is your job. I seem to recall that we had some spacer issues as well. I think we ended up putting two spacers on one shaft. The cases should go back together smoothly and easily. Are you sure you're not resting on the countershaft? Anyway, here you go:

• 

• Were you SURE to get the balancer shaft timed to the crank properly. See the RED circle below.

• 

• You have to re-sync the jackshaft and crank, the shaft of a 5/16" drill bit fits nicely in the split-gear of the jackshaft.

• 

• This picture shows the second gear shift forks, old and new as well as the detent levers, old and new. You can see that the dogs on the old fork are smeared and the fact that they got smeared allowed the body of the fork to get a wear mark from touching second gear. You can see that the new fork has a "heal" to it and is polished. You can not see the hardness test marks on the new part in this photo. The old detent lever shows wear. This happened because the rivet holding the wheel had gotten VERY sloppy.

• 

• This shot is the other side of the shift forks, clearly showing that not only are the new parts polished, but they were hardness tested TWICE. (Those two small dimples are marks from a Rockwell Hardness Test machine.)

• 

Thanks, the book and sharp eyes got this figured out. The first photo I took the washer with the yellow arrow pointing to it is wrong. It does not go there it goes on that shaft AFTER the cases are back together. It is a shim between the case and clutch basket bearings. I have the motor together and back in the bike now it just hooking up things and doing a couple more modifications yet. Should be riding it by next Monday at the latest.

Rest is to TBA

Additional Notes for Clutch Nut Removal if Required

• Never done this job but to keep the rear wheel from spinning try to find a wall or curb to back the bike into. The extra friction on the wheel might keep it from spinning. Good luck. Brad, N. CA., 2001 F650GS - Inmate #1002

• What about using a impact wrench? I have a cheap electric one that is sold for removing tire lug nuts and plugs into a car cigarette lighter receptacle and supposedly produces about 200 pound feet of torque. Maybe you could rent a real one at a rent-a-tool shop. In the mean time, soaking the nut with penetrating oil overnight couldn't hurt. Richard #230: 1997 Funduro

• Drill a set of small holes in the nut, all in a row. Then take a cold chisel and a BFH and break the nut off. Flash #412

• The impact wrench didn't to it either, might try breaking it off with chisel and BFH. You guys that have done this more that once does it get easier after the first time off? I made a tool to apply pressure to the clutch plates so now I need a TDC bolt and maybe a Mapp gas torch. Perhaps the wrong LocTite was used on your unit during assembly. In any case, it will only be as difficult to disassemble next time as the effort you apply during reassembly this time.

• Condition of the Bike: Right now, I have the left crank case cover off and the water pump and clutch removed. I also have the alternator/stator cover off. Procedure: Install TDC Bolt Have girlfriend sit on bike apply back brake (maybe I need to put the clutch back on?), and put it in gear. Have friend steady bike. Heat alternator/stator bolt and only that bolt (what should I NOT do here?). Apply breaker bar with 30 mm socket. Increase heat if it doesn't budge. Repeat procedure with Clutch Nut.
  
  What to buy:
  Large 1/2 inch breaker bar (I'll get this at Sears).
  Heat gun (I'm more comfortable with that than a blow torch). What should I look for? Would Sears have one that would work?
  
  Questions:
  I assume that both of these bolts are "lefty loosy" (excuse my technical jargon).
  Flash: Mine is also a 98. Was there Loctite on your bolt for the alternator/stator?
  Which bolt should I take off first? Should I put the clutch back on in order to help with this?
  
  Of course, if I can't get these bolts off, I have to take in into the dealer. At this point I'd have to reassemble what I've taken off. In fact, I'd need to replace the washer behind the clutch nut since I've already flattened it. The dealer is gonna love me (tried the repair myself, and couldn't get it, read $$$).

• Some bolts cannot be undone alone - you may need a strong and beefy assistant to steady the bike and hold the brake, and you'll need a proper breaker bar (extra long socket wrench). If it's assembled with Loctite 243, use of a heat gun (or careful use of a propane torch ON THE NUT_NOT_THE ROTOR!) may be necessary. If a previous mechanic mistakenly used Loctite 648 (per OEM) or Red Loctite, serious heat will be REQUIRED, not optional. The next level involves use of a large commercial air impact wrench for : removal, however, use of heat is still recommended, as if there is Red Loctite in there and it's not softened with heat, you can break things or rip the threads right off the assembly. (Not likely in this case with a hardened crank, but you never know.) If heat AND an air wrench won't get it... eww. If you have the proper wrench setup, don't be afraid to get the nut up to 100 degrees centigrade (212F), maybe even 225F. No higher or you start to : ruin seals, and the magnets in the flywheel don't like excessive heat either. Best to start off organized, all tools in place, a dry run, quickly apply massive heat on the nut with precision, remove and cool down with a fan.

• You have a gearing DISadvantage on the bolt by whatever gear you have it in when you go to loosen the countershaft nut. You have a disadvantage of only the primary drive when you go to loosen the clutch basket nut. The alternator nut is ON THE CRANK and you are reefing right on the bolt. But... what're you gonna do? You HAVE to hold the crank somehow. Putting the clutch back together is one option. An impact wrench on the rotor nut against the TDC bolt is the only other one I can think of. Oh... I suppose you could drill the nut and break it off with a chisel if all else fails.

Can I remove the alternator after pulling the motor ?
by XtreemLEE#1188 & Flash#412

Read also the Timing Key/Flywheel Removal FAQ

Q. I need to dig into my transmission to replace a couple of shift forks. I would like to pull the motor this weekend but do not have the special alternator puller yet. Is it okay to pull the motor first then pull the alternator with the engine out ? From reading the "removing the motor from an F650 classic" it looks like its okay to do that would like conformation from someone who has done it.

A. Yes you do need to remove the alternator. I finally split the cases on Saturday. In order to reach one of the bolts holding the cases together you MUST remove the alternator and a couple of gears coming from it.

See the pic with the circles around several of the critical bolts that must be removed to split the cases. I circled the ones behind the air filter as well as the ones behind the gears which you must remove the alternator to remove. Also, that one between the oil filter and the alternator case can easily be forgotten.

• Note to self and others doing this: Buy the gaskets, head, case, right side case and left side case, just in case they tear. My motor is going to sit for another week while I wait for gaskets. That is okay, I need the rest.

• If you do not remove the head from the cylinder, you do not need a new egregiously expensive head gasket. Only pull the nuts off the studs. Do not remove the bolts that go up from the cylinder into the head. If you DO pull the head, do NOT reuse the head gasket.

• By the way the F650 book tells you to grind flats on the alternator tool, then tighten the bolt running through it and pound on it (the bolt) with a hammer. It says "10. Secure the outer portion of the tool with a crescent wrench and turn the tool's center bolt with a wrench. Turn the center bolt until it is very tight against the end of the crankshaft. Tap the end of the center bolt (not the rotor as is will be damaged) firmly with a hammer. Repeatedly tighten the center bolt and tap the bolt with the hammer until the rotor disengages from the crankshaft taper." That didn't do sh**, tried that although, but ended up using the impact wrench which just spun and popped it off. Continue till it comes loose. Bull, I realize you are taking a chance here but I used my air powered impact wrench which I think is an absolute necessity if tearing down an F650 motor. It popped the alternator right off. Does it really say "pound on it with a hammer"? When using nearly any puller, it generally works best to load the puller and then strike the puller bolt a single hammer blow to shock the assembly free.

• Another trick when trying to reinstall said alternator. It didn't want to go back on, because of these little tabs in the hub of the thing. Have someone spin the gears to the right of it by hand and it drops right in. That had me and my brother pulling our hairs out trying to figure out how to get it back on without damaging anything, spinning the gears helped it fall in place. Refer Timing Key/Flywheel Removal FAQ for additional details of Flywheel replacement.

• The F650 book tells you to grind flats on the alternator (puller) tool. (The tool Flash got came with flats)
  

• Yes but if you follow the book because of lack of a FAQ you pull the head, since this is my first time I pulled the head. Well for the cost of a new head gasket I got to clean the carbon build up off the head. By the way 19,000 miles and very little carbon. I see now that it could have been done without separating the head from the cylinder.

• Splitting the cases is pretty easy, although having the wrong side down and having transmission parts fall out as you split them had me sweating bullets for a bit. I am mechanically inclined but doing this is a stretch for me, the next time I do it it will be old hat. I have a 72' CL350 that will be next on my list I thought I would do the $6000.00 bike before risking the bike my father gave me for free. I really am just taking your (Flash's) advice and trying to save money, understand mechanics, and developing a better zen quotient with the bike. Because we risk our lives on these mechanical contraptions every time we go for a ride I think you should be one with the bike. Just like a woman you need to undress it and check out every nook and trannie....;-) You are correct about the price of the head gasket, ouch... If my wife's bike needs it motor pulled then I will for sure write a splitting FAQ, of if I do a crappy job and have to pull the motor again I will do it. I think this site which I am a paid member has the best FAQ's period. The only place that even comes close is IBMWR.com and for 650 info they link here.