I bought a 96 r1100RT that would shift fine but no power to rear wheel. I broke down the transmission and found a sheered intermediate shaft. I replaced it and the bike ran fine. If you replace bearings you will need to check the shims and make sure there is no slop. If you do not replace anything the shims can go back as they were. Since I replace the intermediate shaft I had to re-shim so I picked up a digital gap gauge and it worked fine.
If I remember correctly some were replacing the M97 input shaft with M94's because they did not have as many issues.
A lot of good info here. http://largiader.com/tech/oiltrans/