I am on my 4th 68RFE trans in my 08 Cummins + converters One thing the Dodge TCM does is a long term CVI re-learn process. This can take weeks or months depending on how much you drive. I wonder if your TCM does the same thing. I finally bit the bullet and put in a NAPC heavy hauler and I just baby it. I have a tuner set on tow mode and I just leave it alone. If I change the tune on my minimax the trans will re-do the long term CVI process. I still get some hard 1-2 gear shifts/codes but it seems to be holding up with no problems towing.
Regardless I have spent 14ishK on this stupid old truck. Biggest financial loss I have had in my life. Sucks. You might just need to put some miles on the trans and it will smooth out over time.
Machining, Fabricating, Welding etc.