You don't need to replace the rear axle but you will need to be able to adjust the pinion angle to work with the SYE kit. As for which size? the shorter the kit the longer your drive shaft can be which on a short wheel base vehicle is always a plus. With only 2 inches of suspension lift I'm surprised you needed a transfer case drop at all.
The transfer case drop should have come with a transfer case shift linkage relocation plate to compensate for the shifter, you will probably still have to adjust the linkage if you installed the relocation plate.