Well,
Dropped the motor yesterday and pulled the trans. Absolutely nothing wrong with the forks. However, 1st gear will not turn in place on the output shaft. There is some heat scoring on the outboard side of it, and the washer is chewed right up. There is also a bent up retainer (from the washer I'm assuming on the inboard side of the gear). I can't get the gear pulled off the shaft, even with heat, so it might have to be pulled.
I'm going to pull the jet from the oil jet to that bearing and check it out to ensure it isn't plugged and also ensure that the gallery to that jet isn't plugged.
Looks like I'm gonna get the trans built with a heavy duty output shaft, undercut gears, and beefed right up. Going to do new shift shafts and forks as well.
Nothing is wrong with the cases or anything else! So I'm in the clear there.