Well, I think the Jeep is fixed. Stupidest simple thing too. My custom intake rubber boot was collapsing under load starving the engine of air. It must have gotten hot enough under the hood that day to soften that boot and it eventually fully collapsed.
How I found it: The tranny shop had it for 3 days and couldn't find anything wrong nor could they verify the symptom. The night I picked it up, it was fine. The next day, I noticed it acting up but wasn't as bad as before. The day i did the gears on the JK, my wife had the WJ. She noticed under easy or moderate acceleration, it was fine, but under heavy acceleration, it wouldn't pull. So a few days later, we took it back to the shop. They checked fuel pressure under load, checked for intake leaks, all was good. They did verify the symptom but said it wasn't transmission related and basically said it was out of their realm. I was happy with the time they spent on it though.
So I picked it up this afternoon with a hunch that it was my catalytic converter. It felt like that Everytime it did it. But the cat is only a year old. Did a little reading online and found a few cases of people damaging a cat after a deep water crossing, basically it cools too quickly and cracks then plugs. I have a good OEM cat at home so it wouldn't cost me anything to swap. The Jeep acted up several times on the way home. However, when I got the Jeep home, I decided to hit the throttle hard while in park and look at some things. I noticed immediately the intake boot was collapsing a little. The more I opened the throttle quickly, the more the intake collapsed. So I took the whole thing off and put a cone filter right on the throttle body. We took both jeeps up the mountain about 15 miles and I drove it hard. Never acted up once. Oh, and my power is stronger and gas mileage indicator increased by 3 on the display. Sounds like I've had this going on for awhile, just finally the tube softened enough to leave me stranded.
An expensive lesson. Thank you all who hung out and tried to help last weekend and for Ben driving my wife and kids home while I waited for the tow truck. We could have fixed this thing up there in about 30 seconds.
My next plan is to find an OEM intake system and install it. However I will have to build a custom washer bottle and relocate it.