As far as the transmission goes, the auto in that Jeep is the super strong GM built TH400. A simple shift kit and a TH400 will handle some serious abuse WITH big tires and power.
The transfer case is the Quadratrac. It uses an offset rear output design which is weaker than a straight through, plus it's aluminum and chain driven.....so yes, it has gotten a bad reputation. I like it though. I won't be swapping it into any of my Jeeps, but it does deserve some respect and it has a few neat features. Part-time conversion kits can be bought with a 18% overdrive or underdrive built into them, which is kind of neat. Most problems come from not replacing the chain after it gets worn, and not using the correct fluid. There is really nothing wrong with it, you just need to perform routine maintenance and stay on top of the cahin stretch issue and they hold up fairly well.
With that setup, you can swap the axles from a quadratrac equipped pre1980 SJ and have D44s that match the offset output of the Tcase.