I have used the LS2 TB with adapter harness on some C5 Vettes, they all worked fine but none of them is boosted. IIRC the TB is reversed to make it fit so the blade may be moving or something is upsetting the TAC. The strange thing is that the codes you get are airflow related, not electrical.
Hope you can go to the track and test, I may have to boost a 03 Z06 with a Fast intake and LS2 TB soon.