I need to replace the seal on the gear shift for a 94 YJ AX-15 tranny. How do you get the shift arm (arm visible in the drivers compartment) off the shaft that comes out the top off the tranny. There appears a large square nut at the base of the shift arm but doesn't seem to want to turn. Any help is appreciated. None of our manuals give these details.

Push down on the spring loaded retainer and turn it counter clockwise. Once you turn it about a quarter turn the stick will come out.

I need to seperate the upper shaft from the shaft that fits into the tranny. I can get the entire assembly out of the tranny without problem but how do you replace the rubber seal that fits on the top of the tranny?

These two shaft parts come apart by use of force. There are no threads, it is a jam fit. If you look closely at the bottom of the upper shift shaft, where it fits over the lower section, you can see that it's a rubber sleeve inside the round hollow bottom on the shaft. There's a square steel part inside this, which fits over the square upper end of the lower shaft section. (This is startin' to get complicated!) Anyway, it's just a lot of friction holding them together. Pry really hard, and be careful, you could get hurt here.
Good luck!
AJ