Just finished rebuilding my 01 transmission. Not too bad of a job but one thing kind of annoying about the service manual is about the shaft nut on the countershaft (where the two bearings are, 1 with clip grove) is left hand threads. There is no mention of this in the manual at all, I though I hadn't got the lock opened up properly as it would turn a 1/16 of a turn and stop. turning it back to open the lock up more was quite easy. After two times doing this I figured it out.

I replaced all the bearings and seals even though only the input shaft bearing was bad, also replaced 2nd gear assembly (including syncro's for 2nd and 1st.) Shifts great nice and smooth.
Steve, great tip on the removing the lower strut bolts way better than messing with the lower ball joint. Also for getting the clip back over the bearing (dropping the case gently on the bench and it pops right in place.