Alright so I just installed an AMS turbo back exhaust w/test pipe and ams intake, tuned by Accessport Stage 2 flash. After all of this is installed, I did some pulls on the highway, 1st gear was smooth as usual, 2nd gear starts the issue, once I go WOT it starts to break up at about 3000-3500 all the way up to 7k, not as bad in 3rd but still does it a little bit. Suggestions?

 

sounds to me that the canned tune is not good enough for your setup. I would get it protuned.

or switch to opensource.

 

You could try decreasing the gap on your plugs. That should help.