[olddog]

I'm thinking that maybe the bell housing is not alligned to the pilot bearing. This would cause wear in the pilot bearing and would be pretty hard on the tranny input shaft seal and bearing.

While its out, give the tranny a good look. Maybe have a shop look at it, if you cannot find anyone experianced to come give it a look. The front bearing could be worn.

PS
You need to make certain that the bell housing is aligned propperly to the pilot bearing, before it goes back together. I'm no expert, but I don't think pilot bearings wear out very often, unless something is wrong.