Last night I went to town on the transmission. Took the installed gear stacks and set the pinion depth, measured the tolerances and she's ready to go back together. I changed the front diff to a Helical JDM LSD type (version 5) and changed the ultimate final drive to a 4.44. Also acquired a viscous 4.44 R160 rear diff to match to the transmission. I need to open the center diff and make sure the guts are still in good shape. Following that I should be ready to seal her up and install it back into the car.
The process was a bit painstaking, but I think it should be worth it.