Yep, the transfer case is another gold mine as well. I see the NP241 OR Rubi transfer cases sell for upwards of $1000 easily. There's several on eBay now for $1300+.
Buy them if you can! I just did the rubicon swap last week and I had to pay 3k. 2,500 is about the cheapest you will see. Everything is bolt in except you'll need to get your driveshafts cut a little shorter.
Take the diff covers off and inspect the ring and pinions and the lockers. Should be easy to notice anything if it's damaged.
Obviously keep in mind there's a chance you might have to replace the u-joints on the axle shafts (which are cheap and easy to fix), but really the main thing is just making sure there's no damage to the axle or the gears / lockers.
Again, it shouldn't be hard to tell if the axles were abused just from looking at them.
Get an extendable magnet like the one on the end of a pointer. When you get the diff covers off run that magnet as far up into the case as you can get it. Hopefully there are no surprises.