Well, I put the latest software in, cleared TCM KAM, and adaptive tables, and got her hot. Performed the adaptive drive and now 2nd is extremely harsh and 6th is harsh as well. So I replaced the 2-6 solenoid and went through the KAM reset, adaptive reset, and adaptive drive and she shifts like butter. It looks like I will be replacing a few more, as they come in for service.
I got it. What I found is the app % was at .5%. When at .5%, the truck would start and stall, or surge for 5 seconds or so and then come up and then back down to idle. If I put my toe under the pedal and bring it to 0% it starts normally. I did this probably 20 times to convince myself it is the cause. If it is 2% or more it seemed to start ok. Must be some sort of Idle Validation in the software. When I did the pmi, I am guessing it learned .5% as the new 0, and then when the pedal returned fully, a new 0 was learned. I am fully confident a new app will fix it. I disregarded the .5%, as I thought there was no way in hell it would cause the stall and surge, if anything a slightly higher idle.