I think you are doing all the right things here.....including spilling a bit of oil.....!
I don't know where the crankcase oil level is relative to the rear seal, but it is probably higher than the seals to keep them lubed, so no real problem if oil comes out when you take the flywheel out.
The clutch/pressure plate assembly is mounted with the marks 120 degrees apart so you do have a perfectly balanced clutch.
Oil in the booth.....that happened on my GS which had a similar arrangement to the K-Bike, I don't remember any problems in pulling and replacing the seal, but you should replace the booth, dirt in there=rough clutch action. Isn't there a piston in there that pushes on the clutch rod? that should be very clean and lubed before you reinstall it.
I don't remember replacing the pressure plate bolts, but that was many years ago......! The shop manual for my K1200RS does not say anything about replacing them and it is the same type of clutch.....don't know, certainly locktite but replacement.....
Mind you they can't be very expensive, but they have to be the same exact type of bolts.
Do you have a clutch alignment tool?You can make one using a piece of wood dowel and electrical tape,but I have replaced many clutches on cars and bikes and never used one. If you do not have one you have to center the clutch by sight, looking through the center hole. Pretighten the pressure plate bolts just enough that the clutch plate stays in that position then slide the tranny in there. If it does not go in ,wiggle it a bit. The trick is to have the plate just loose enough that it centers itself.
Once that is done, delicately pull the tranny back and torque down the pressure plate.Push the tranny back in, bolt it down.....done
I hope this helps....