$3500 later, finally back on the road. I took it to a different shop for a second opinion. They spent 3 days looking at electronics and first thought it was the computer. Eventually nothing was found so I had them remove the transmission and poke around inside. It was diagnosed as the torque converter coming apart, sending debris back and damaging other internal parts. So this is the 2nd transmission rebuild in the truck at 155k miles. Hopefully there won't be any issues with it.
Unfortunately the warranty at the second shop is worse than the first. For a short time I thought of taking it back to the first shop, but the fee they would of charged for time spent on electronics by itself or looking inside was quite a bit. All of the diagnostic fees were waived, and the final price was within about $50 of each other, just a worse warranty. Say bye to the front and rear locker funds though.