Oh Boy Ryan,
That is the million dollar question, and here is a two cents answer. As you have done, I was all the way down to the frame. I replaced every seal and gasket on the transmission, transfer case, front and lower part of the engine. The layers of crud that I scraped off told me I had a problem with fluid loss. I was determined to stop all losses. Cleaned all surfaces numorous times. Used gasket sealant and gaskets on all surfaces. I was convinced I would beat the leak....I failed.
Some of my leaks are from my stupidity. Some are from worn surfaces that seals run on. Some are from a poor design on the Jeep itself. I mean, who taps threads all the way through the transfer case housing into the fluid holding area? And only in some areas? (A couple of my leaks are clearly coming through the threads on some attaching bolts.) Heck, I have a small leak where the emergency brake pull pivot arm attaches to the transmission case. I mean...really? That bolt is threaded all the way through to the fluid? Geeezzz!! I was so careful about clean surfaces, but didn't think to put sealant on some bolt threads. To stop it, I would have to drain out brand new, pricey gear oil. Very frustrating.
At this point, I am reserved to the fact that my Willys will always leak a little. And when the winter comes...and I have very little to do, I will chase those leaks. I will likely fail to eliminate them all, but it will give me some more quality time with my Willys.
Tim