YJ's weren't designed to run in 4WD at speeds faster then 50 MPH. YJ's didn't have CV shafts and don't really need them since the shaft is so long the angle is pretty minimal especially since it had a high-pinion. To run a CV shaft you'd need to point the pinion at the transfer case but doing this will screw up the caster. Otherwise, you start running out of phase.
As for the transfer case itself. The TJ's have a better range shift selector which gives them true neutral. That's about the only thing better.