Ah, I'm not the only one that has run into this sort of problem! Same issues here when changing trans tunes. I had thought it was due to accidentally getting dielectric grease on the pins for the main wiring harnesses going into the ECM/TCM. I cleaned them multiple times with QD Electric parts cleaner. Currently I seem to only get one code, U0101 for the TCM. Now, I don't know which of the three wiring harnesses going into the ECM/TCM are for the TCM, but, one of the "lever clips" that holds them in place ( the one closest to the driver side) has a piece of the plastic that locks it in place cracked off so it no longer holds in place correctly, but I have a zip tie holding it at about the same position as the rest until I replace the actual clip. As for now, whenever I load a new tune, which has only been Trans Tunes, I only get the DTC for the TCM communication. Now with that said, I used to be able clear the DTC and the codes would almost immediately return, now after cleaning the pins and getting the clip as close to the same position as the rest, it only happens immediately after loading the Trans tune and once I clear the code one time, it does not return. So, I feel you're pain. Let me know if you figure anything else out.
Side note: I am only talking Trans tunes and you are dealing with what appears to be both Engine and Trans Tunes, so from my research on the trans side I came across information regarding checking your ground wires if the rest of the wiring is ok and if all that checks out, then the ECM/TCM will need to be tested. I am a garage mechanic, so take it for what its worth.
