This thread has been a great help. I just picked up a '95' R1100GS with 15,000 miles on it. Having heard about the transmission I also found a '99' M97 with 13,000 miles on it.
I do all my own work on my bikes and rebuilt the transmission on my '96' R1100RT.
Since the bike has been garaged sinced '98' I will be going through it with a fine tooth comb and this will include a spline lube. Would the recommendation be to change out the old M94 with the M97, Run the M94 until it has a problem and then put in the M97 or swap out the weak input shaft of the M97 with the input shaft of the M94 and then put in the M97.
Any insight would be most helpful.