Probably should have mentioned that the car is stock except for exhaust and pods. The plugs were done when I had every one over. The battery is brand new also, as I have experienced what they are like when the battery is almost gone. The aac valve was cleaned very recently as I had to change the 3 little pain is the ass hoses at the back of the block. The apexi was set to a standard mode and was in the car for about 3 months without a problem. There were no error codes and the hand controller was saying everything was running normal.
I guess the reason I posted on here was for opinions, after all, I assumed this site was for this kind of thing as well as many others. Didn't really want to now toe it to some one and then it costs me 3k just to find out it was a simple part. I have done a crap load of work on this already by myself which would have saved me thousands so far. This was also why I had such an extensive description, even though the problems may not be the same thing.
Thanks for your help guys, I will check the coils, ignighter, CAS and injectors. I will let you know.