Looks like you have your answer, but to be clear, I don't have any experience with either and was basically throwing a hail mary.
I forgot to ask earlier, have you drained/replaced the fluid? I did a little more digging and it's definitely pointing toward clutches or seals. If the clutches are bad you might see evidence in the fluid. To tell if the seals are bad you have to drop the valve body (not that hard) and do an air test to listen for excess blow-by when the clutch applies. In either case you'd need a rebuild which would replace the clutches and seals as standard practice.
But I'm also focusing on what the shop found. There is still the funny business around the computer, and your other thread where your computer in WranglerFix's jeep also caused flaring, right?
they said when they put my TCM in their jeep it caused a flare from 3-4. They told me to send it back and they will take a look at the one they sent me and send a new one if need be. He also said he tweeked something with the PCM.
