Is there a track out there by Cambidge that you are running at? I wish you were a bit closer, I'd be able to help you out on setup and launching.
Getting off the line is the most important thing, ever. Get that 60' down and you'll be in good shape, but I know those big 20's a depending on what rubber you have might not make that possible. What psi are you setting the tires at? If you are dead set on getting in the 12's, do you still have your stockers? It will look really stupid but those light wheels, aired down will be better than your big dubs.
The mph is there, so you are making power. The 3-4 shift could be ecm tuning, but you want that shift to have the largest defuel/slowest shift, the most parts are moving on that shift.