Okay, like drew said ^^ the Cobb map you are running is SPECIFICALLY for the AEM intake and a DP/TBE. Nothing more. The MAF scaling for your CAI is different than the parameters set on your map. Your headers have a different flow rate and pattern to the turbo which optimizes spool time, which your map is not adjusted for. Your QTP cutout is okay, you don't need to do anything about that.
We cannot stress enough how much you NEED a custome tune. There is no other way around it.