Michele St.
Glad you found the problem. One thing that is very important that I hope you or your mechanic looked at is the shape of the stub part of the input shaft where it rides on the pilot bearing. Quite often, if the needle roller gets oblitterated, like you said, it can score and damage the input shaft. If you replace the input shaft, fine, you fixed the problem, if you didn't, the scored shaft can take out the new needle roller pilot really fast. This is primarily why we designed the kevlar bushing so it could ran with a scored shaft.
Just trying to give you a little heads up.
Peter