You can verify the input and output shaft shimming without disassembly. For the output, pull the flange and see if you can move the shims with a pick. You can even bend a feeler gauge and see how you did. For the input, warm the cover slightly and see if you can push the shaft up and down. If it moves, you'll have to go back in.
It is difficult to get the box to shift well on the bench; you can't spin the shafts fast enough to align the shift dogs.