Alpha N Tune Struggles

Hey everyone, this is my first post on e46Fanatics, I have been active on BimmerForums, so be gentle. I wanted to throw this out there and see if anyone else has had the same issues, or even resolved them in their experience. I have an 05 e46M3 - CF AirBox, MAF Delete, Pulleys, and an Alpha-N Tune. I recently installed FABSpeed Headers, deleting the CATs. Once the Headers were installed, I kept having a misfire, and we've been trying to adjust and retweak the tune to reflect the CAT Delete and Header Install, but we're still having Misfire Issues. I'm in the PA Area. Any suggestions, war stories (good or bad) would be greatly appreciated