I need to pull my R90/6 tranny to replace the rear engine seal this winter. I am sure there are a lot of us out there that would like to know the sequence of tasks and what the "couple of specialized tools" are.
This will be a long one... So I'll break the reply into two parts: Tear down and reassembly.
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 lockwashers, 4 driveshaft bolts, 6 clutch bolts, a 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 [see Links]), a 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), 27mm or 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. Before you forget it, 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 one on each side 10mm nut that secures the battery box 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 lockwashers 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 27mm or 1 1/16" socket to loosen lock nuts on swingarm 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 interfer and have to be removed (mine do).