Hmm. I don't know how or if SRM logic is involved in this, but the fact they've had much of the car dissembled makes me wonder if in the course of all of this work, a sensor was damaged or something...
I'm not sure who tuned your car, but if the ROM file doesn't match the ECU, it simply won't work -- in fact, it can brick or lock up the ECU. Meaning, if the tune matches the ECU and the ECU matches the car, all should be good. I don't think you can do any mixing and matching.
Now "pinched" ECU wires causing weird glitches -- of that I don't know. That's weird. I've never heard of that before. Unless they was damage in the wiring causing connection problems or something.
Either way, it boils down to that fault code points to a specific sensor malfunction, so that is where they should begin trouble shooting. If in the course of doing that they find a damaged ECU wire, okay, fair enough, but the good news is all of this should be easily deducible and fixable (albeit very annoying!).
Good luck!
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