Aullen just because you had a bad experience with the installer doesn't mean there was an issue with the tune. Did you do enough exploring into, and talking with your installer before he took on such an adventure? Had ever done that install before?
Personally I'd call your installer back and force him to make it right, and re do the tune. I don't think it would mean to re install the entire exhaust. Than, just reflashing the ecu to stock then install, fix the issue with the adblue then, reflash the ecu to stage 2.
If he won't fix the issue then post it on TDIClub for people to avoid going to him.