I'll keep it short and sweet. Basically I can go out and do 3rd and 4th gear pulls and hardly have any issues with my AEM pulling timing. Then lets say I will start and 2nd and start ripping through the gears I can feel the car stutter in 3rd and 4th where its pulling timing. So what is making the car do it if I am ripping through the gears but not doing it when I just do individual gear pulls?

 

A few things - (1) you could have shift knock, (2) you could be hitting different loads, and (3) your tune could be a the edge and the additional heat soak is causing the knock...

 

I am not sure what "shift knock" is, but I would lean toward it as being the most probable of the three possibilities that you mentioned cij.