Welcome to the forums
I'd suggest posting pictures up to a photohosting site and then linking them here so that we can get a look at what you're talking about, which will help us understand the overall configuration and lead to some troubleshooting.
In the description you indicate you have a front 44 with an air locker and a rear 44 with a full spool. You've got a pretty extensive list of modifications which is awesome, however may be impacting the "streetability" of the Jeep.
That spool in the rear will wreak havoc on the transfer case, yes - but the UJoints will suffer first
There is always a trade off in the modifications you do.
My first line of suggestion if you've checked the transfer case is to give the drive shafts a good crank while it's on the ground and note ANY Play in them. That play will turn into a lot of racket, especially under load on a hill.