As I mentioned before, all Jeep Wrangler TJ NP 231 cases from the factory are the same except for the input gear. The automatic has a different input gear from the factory than the manual. But that is the only difference whatsoever. Other than that, the transfer cases are the same.
Input gears are a very simple swap as long as you remember one thing. Around 1995 or 1996 (about same time New Process became New Venture) they changed the tooth profile on the planetary gears, the ring in the case half, the planets in the cage, and the sun on the input gear.
So what I am saying, is that it doesn't matter what transfer case you buy, as long as it came from a 1997-2006 Jeep Wrangler TJ, and as long as it's not a Rubicon transfer case (which is a NV 241).
The worst you'd have to do is swap the input gear if you bought a transfer case from a manual transmission model, but that's easy.
As for bent driveshafts, if the transfer case locked up and grenaded, then yeah, I would bet your driveshaft is done for. Post a picture, it will be pretty easy for us to tell!