Just picked up a pair each of the clutch release shafts and the actuation arms to be dropped into both bikes here shortly. Have a couple of questions before I get started:
With good oil flow and the proper level, can the plates stick together?
If so, would there be enough tension to break two or three clutch cables if the plates were sticking?
Since I will have everthing apart should I pull the plates and rough them up?
Has anyone else ever stripped the teeth off of the actuation arm, or does it normally just happen on the release shaft? I'm missing one on the shaft itself and three on the arm. They sheared off all at once, was very noticable when it happened,

I guess the real question, after all of that (LOL), would be how in the hell do your ensure that the teeth on the arm and the shaft are going to align and remain that way while you are fighting to get the side cover back on?
I've replaced plates several times, replaced springs several times, and there always seems to be some resistance at the shift lever shaft o-ring. I start out with the teeth in alignment , but am not sure that they remain that way throughout the process,which may be my whole problem...

 

I think I know what you mean. I have had the clutch cover off probably four times total on my two bikes, and it has never once gone back on without need of gentle encouragement from a mallet. If it doesn't go back on after moderate taps from the mallet, then I know that the teeth are not aligned correctly. As I recall, the shaft (i.e. the "D" shaped piece coming out from the clutch plates) wants to turn as you are trying to put the cover on. I believe the flat part of the "D" needs to face the 3 or 4 o'clock position in order to line up, but it wants to flip to the 6 o'clock position. What I do is slap some grease behind it, so it will stay in position and slide into the "D" shaped hole on the inside of the clutch cover. I am not sure if what I described is your problem, but that has been my experience, for whatever it is worth.

 

I always put a dab on grease on the shaft coming out of the clutch to ensure that it won't turn after getting it in the proper position. Its worked everytime for me.