Doug,
Did you test the movement of the shifting forks with the shifter in the tower (move through all the gear switching ranges), before resetting it onto the transmission?
On the same thought, did you manual push the gear clusters through their motions to confirm nothing was binding and all gears where able to move through the full ranges?
It can be a tedious process and takes patience to push/manipulate the gears and then turn the input shaft to make sure everything is aligning correctly, but that is also something that should have been done before reinstallation.
If you did these things, the only other thing I can think of off the top of my head is the shift forks didn't go into the correct places on the gears when you put the tower back on. There's a good possibility that one of the gears moved during the install.
I know "that" can happen as I did it myself once or twice.
