The Jeep CJ 2.5l engine is actually a GM engine, using the Small block Chev bolt pattern. Use any GM transmission you like and buy the adapter to adapt it to your Tcase......OR......Use a GM engine ,trans and tcase and just swap out your rear diff for one that is centered.
Personally I'd stay away from the T90, I've rebuilt lots of them and they're marginal at best, use something made AFTER you were born, it'll be easier to keep on the road.
Check your PM's, a friend of mine has a flatfender project that needs assembly that sounds like just what you're planning on building.