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Rear Engine Seal Replacement on a R90/6

(This procedure will work on most R-bikes..however, some of the procedure will be different depending on Model/Year, check you Haynes or Clymer manual for specifics related to your bike- ed.)

by Matt Parkhouse –
(original publish date unknown)

I used to be able to R&R a gearbox, in a good shop in an hour. To do what I’ve described here, working in front of the house (on a warm day), I would budget 3-4 hours. I have done this task maybe 100 times over the last 20 years. I certainly would recommend using more than this description to under take this work. A Haynes/Clymer manual at the least, a friend who has done it is best.


Parts to have on hand…

  • Rear main seal, oil pump
  • O-ring
  • Oil pump cover and 4 bolts (upgraded since /6 series),
  • 5 new flywheel bolts
  • 4 driveshaft lock washers
  • 4 driveshaft bolts
  • 6 clutch bolts
  • New driveshaft boot if the old one is cracked or leaking

Special tools…

  • Clutch compressing screws (you can use bolts and nuts-less handy but works OK, or get from Ed Korn)
  • Flywheel brake (make out of bar stock or get from Ed Korn)
  • Rear main seal installer: from Ed Korn
  • 6mm allen drive on 3/8 socket, torque wrench
  • 10mm-12 point box end wrench ( I like Snap-on’s)
  • 1 1/16″ socket (turned or ground down on outside)
  • Micrometer or calipers
  • Slide hammer with hook attachment
  • Impact screwdriver with large Phillips bit


  • Place bike on center stand (if a “Ride-off stand”, block up on 2X4s), you want to be able to turn rear wheel freely.
  • Drain gearbox if work is planned on it.
  • Drain driveshaft as oil will spill when it is disconnected.
  • Remove gas tank, set aside out of way.
  • Take carbs off cylinders and hang over front of cylinders, out of way.
  • Open seat, tie or prop open, take out tool kit tray and place with gas tank.
  • Important! Remove points cover and place a short piece of metal (cut-down Allen key is best) in Allen slot of alternator. Put engine at Top Dead Center (TDC) before doing this. You want to firmly but gently jam the crankshaft to the rear by replacing the front cover and putting pressure on the alternator/crank assembly. Failure to do this can result in the crank moving forward, after the flywheel is off and pulling an endplay shim off it’s posts INSIDE the engine. You REALLY don’t want this happening!
  • Clear away air cleaner housing on both sides.
  • Remove battery.
  • Remove the 10mm nut that secures the battery box on each side to the frame, this allows you to tip the battery box back a little.
  • Take off the forward hose clamp the secures the driveshaft boot to the output of the gearbox. This exposes the four bolts that secure the driveshaft to the gearbox. Rotate wheel so you have a good shot at one of them. Apply rear brake to lock up everything and undo one bolt.
  • Rotate wheel and repeat for other three bolts. You want a magnet on a stick tool handy, in case you lose track of bolts or lock washers in the driveshaft housing.
  • Take out pin that rear brake pivots on and allow foot brake lever and rod to drop down.
  • Use ground down 1 1/16 socket to loosen lock nuts on swing arm pivots. Use 6mm Allen to take out pivot pins.

You now should be able to pull back driveshaft and rear wheel assembly about an inch or so. Bag mounts may interfere and have to be removed (mine do).

  • Take off clutch cable (a long lever helps).
  • Take off throwout assembly on back off gearbox (held in with circlip). Check throwout bearing and two flat thrust pieces for wear and set aside (this is sort of a weak point in /6 or /7 BMWs).
  • Remove two bolts on left side of tranny, one long bolt and nut on right side, that secure tranny to engine block.You should be able to pull back on gearbox and lift it up and out on left side of bike. As you do this, pay attention to neutral switch wiring on bottom of the box.
  • Gently pull off the two wires (It’s kind of easy to bend and break the push-on connectors on the switch). You now have the gearbox in your hands.
  • Pull out throwout rod from input shaft and set with other throwout pieces. Set gear box aside.

To get clutch out, remove every other bolt visible at back of clutch assembly (3 of 6). Install home-made or purchased compressing tools in their place. Tighten down, then pull the other three clutch bolts. Loosen the compressing tools equally until the clutch is loose and rattly. Back all the way out. Pull out assembly as one unit, mark with chalk, ink or small scratches; both pressure plates and flywheel, so you can reassemble as it was originally balanced.

Check clutch plate with micrometer or calipers: replacement point is at 4.5mm thickness, new plates are at 6mm. Set aside.

To remove flywheel:

Is engine still at TDC?. Install flywheel brake in two of the clutch bolt holes so that wheel is locked against side of engine block.Remove the 5 bolts and gently lever the flywheel off the end of the crankshaft. Heating helps sometimes. Put it aside with brake still attached.

Now you see the oil pump cover. If you see bolts with 6 point heads in flat recesses in the cover: it has been up-dated. If you have Phillips head bolts, you have not been updated, an impact driver helps in the latter case. If there is no sign of leaking, just check the bolts for tightness (8 ft. lbs.). They are often loose. If you are replacing a leaking rear maim seal, yank out the old one using a slide-hammer with a hook. Even though you have braced the crankshaft from the front, avoid putting a lot of force on it as it is now able to move forward. The bike is now torn down all the way for these tasks.

Now is a good time to clean all this stuff. Part 2 will cover putting it back together.

Replacing Seal and Reassembly

More specialized tools:

  • BMW swingarm grease
  • Fitted grease gun or chain sawnose-wheel greaser

We left the bike torn down to the rear crankshaft. I like to use spray carb cleaner to clean parts and the usually grungy clutch compartment. Not unusual to go through 2 or 3 cans on this sort of job.

The new rear main seal goes in, using the installing tool. BMW makes a nice one, so does Ed Korn. Hopefully you noted exactly how far in the block the old seal was; try and get the new seal to the same level. Since we have already tightened the oil pump cover or replaced the O-ring there.

Replace the Flywheel

I like to clean up, again, with carb cleaner, and then touch up the markings (“F”, “OT” and the dot for full advance) with a white paint stick, while I have the flywheel in my hands. The flywheel goes back EXACTLY as it came off. Is the OT mark where it was when you took it off? New bolts are in order here, but some
folks do reuse the much heaver /7 bolts (I have). Bolts are clean and dry. Tighten to the recommended torque.

Remove the flywheel brake and release the brace at the front of the engine and make sure the crank turns easily.

The clutch goes back next, with cleaned up parts and maybe a new clutch plate. I reuse these bolts without out problem, others like to replace them. Torque to 16 ft. lbs.. There are clutch centering tools, I use them but if you don’t have one, get it “pretty close” to centered. The first time the clutch is used, the plate will line up anyway.

The gear box is next, with nicely cleaned up splines on the input shaft (the part that goes into the clutch plate). Put the throwout rod back into the hollow input shaft, tapered end toward the clutch, with a bit (small bit) of anti-seize on the end, with a bit of grease or gear oil on the shaft of the rod. Coat the splines with a thin layer of anti-seize (a do-every-20K task) and install the gear box in the reverse of the movement you used to take it out. Do pause part way into it and hook up the neutral wires to the switch on the bottom.

The two bolts on the left and the long bolt with nut on the right reattach the box to the engine block. The throwout assembly goes back to the rear of the gearbox. Loosen and back out the adjuster bolt a little. Be sure to coat the pivot pin with grease and put a little grease in the cup where the throwout rod contacts the throwout lever. Do you need to replace the little rubber boot that covers the cup? When you have properly adjusted the throwout lever and clutch hand lever, the throw out lever should be, or close to, parallel to the back cover of the gear box.

The driveshaft goes back now. If you are putting on a new boot, now’s the time. The “OBEN” marking goes on top. The pivot pins go back into the frame and swing arm mounts. Some folks use calipers to measure the equal spacing. I
find eyeballing is fine. Back off the lock nuts a turn or two. Using the 6mm Allen tool in a torque wrench, tighten both to 14 ft. lbs; then back off and retighten to 8 ft. lbs. This is the preload for the tapered roller bearing of the swing arm. Tighten the locknuts, using the 1 1/16 socket, to 75 ft. lbs..Give them a generous shot of grease (until it appears, emerging from the seals). Reassemble the rear brake set-up first, as you will need this to lock up the driveline for tightening of the bolts. Then, with new bolts and lock washers, reattach the driveshaft to the output of the gear box. Get all four bolts pretty well in by hand, then one by one, rotate the assembly by turning the wheel as you use the 12-point 10mm box end to tighten the bolts. There are devices for measuring torque, I just give a good grunt to the wrench. In a pinch, I have reused the bolts, it’s REALLY a good idea to use new lock washers every time.

  • Reinstall the hose clamp that anchors the drive shaft boot to the gearbox
  • The battery is replaced
  • Replace the air cleaner housing halves and the air filter. A little silicone spray and some needle nose pliers really help to pull the crankcase vent hose into the right hand air intake.
  • Reattach the battery box to the frame with the two 10mm nuts.
  • The carbs go back on the heads and air cleaner housing. If you were gentle with them and didn’t pull on them or bang them around, you shouldn’t need to rebalance them.
  • Fuel tank back on
  • Tool tray back in
  • Replace any drained oil and you are all set


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