I'm not trying to be a tool but why the hell would anyone in there right mind change the entire harness over to accomadate a bolt in plug and play swap, you say your throwing a code...the only way to do that is to be using the OBD 2 ecu in your car...the person who did that swap really should not have gine through all this trouble. When you wired up the VAFC you did look for the OBD2 corresponding wires and verify each wire w/ a DMM correct...if not you my friend have a headache and a wiring issue...I wish I was closer I could probably fix that for you.
ASE-automotive service excellence-not the HARDEST test to pass so that doesn't mean too much. Find an EXTREMLEY competent installer in your area and have them double check the wiring. Good luck.