Just got caught up. Sorry to hear about the gremlins. Couldn't imagine dealing with other people working on my stuff. While I'm reading I'm going thru the scenarios in my head of what your issue might be. Hard to diagnose thru my phone screen but when I heard that they said either throttle body or TAC module, I said to myself, no shit Einstein. Problem is now that you bought the TB it's yours. They don't normally refund on electrical parts. Replace under warranty, yes. And you won't get shop to eat it either. At this point they are gonna tell you that the TB was a problem and remind you of how good it was after they replaced it. They'll tell you it may have not been the only problem but it was a problem just to save face so it doesn't appear you spend $300 for their misdiagnosis. So calm yourself. Don't curse out another tech, well at least until they can solve your issue. They will want to make you happy and feel all warm and fuzzy so they can keep a customer and you won't go on social media or Angie's list and bad mouth them. Which you really should do anyway. People make mistakes. Especially with electrical crap. This could be something as simple as a ground issue. I can't remember who mentioned it, but I agreed when I read it, need to ohm the wires to see if you have a bad wire. Also check that harness that you said you wiggled when it started reading. Maybe there's a ground terminal that was suppose to be attached to one of the bellhousing bolts but the trans guy missed it. It could be getting a connection sitting on or against something metal but when heat, moisture or both happen it loses it.
And when your battery is disconnected for extended periods of time it WILL NOT mess up your tune. What it does is resets your long term fuel trims and it takes a few drive cycles to learn them again and adjust fuel accordingly. Short term fuel trims are instantaneous depending on what the O2 sensor is telling PCM what it's doing. When STFT are either pulling fuel or adding fuel the LTFT step in and make appropriate adjustment so the STFT don't need to swing so far. Kinda makes adjustments so the computer doesn't have to think so much.
Awesome read as always Tony. Sorry for being absent for so long, I may have helped you diagnose this before seeing a mechanic. Of course, you'd have to be willing to get dirty. Hahaha.