Wiiiiierd Problem...MAF causing trouble!!!

Hey fellas!! Heres the issue I'm having, hopefully somebody has some insight on this. I have a 01 Silverado, just did a complete motor and tranny swap. I've been doing some tuning in VE so my MAF was turned off obviously. Well while tuning I have no issues at all. When I turn the MAF back on, I get engine misfire code P0300 and my TCC wont lock and unlock like it supposed to. Took the MAF off again, and it works no problem. What gives?? The TCC doesn't even attempt to lock at any time!!