I just did the clean air mod and i also have a power commander so is my pc going to have to be retuned or what.

 

Does it have to be? No. Should it be? Depends on if the original programer just loaded up a generic map or custom tuned it. And if it was custom tuned, did they block the AIR system when tuning as your supposed to or did they just tune with it in place and working. Either way you won't really see any difference unless you have numbers in front of you.