Finally got this into Matt's shop and torn apart. The tranny guts were good and swapped into the 700r4 K case I got from Tacoma. Thanks again. Found out one of the contributing factors was the bolts on the Atlas adapter were loose. While I have a little time in the shop I've decided to tackle 2 problem areas, 1, address every leak on the Heep and 2. fixing the broken hub and outer stub shaft on the front axle. Of course every break is an opportunity to upgrade so I got some 35 spline alloy outers and a short side alloy inner, along with new Mile Marker selectable hubs from All Jeep. Thanks Davy.
The leaks are another matter. I had 4 leaks on the WJT and they were substantial, the tranny, the front inner axle, the rear 14 bolt pinion seal, and the steering box. While the front end was apart I replaced the inner axle seals and will clean, regrease, pack the wheel bearings and reseal. Next I will pull the pinion seal on the rear 14 bolt, put a new seal in, and then add the new pinion guard and axle truss tie in I got from RuffStuff, along with the new heavy diff cover.
After all of that is finished I will button every thing back up, and make sure it runs, then I'll pull the steering box and reseal it. It will be good to get this back on the trail/road again. I want to start the body work this winter.