Not sure what tuner you have but on my DiabloSport InTune I can tweak my shift pressure and shift points (for both minimum MPH for each shift and their WOT shift point RPMs)
On the 93P BAMA tune (one I am playing with right now) at WOT the 1-2-3-4 were all set to 7050 RPM shifts the 4-5 was 6800 and 5-6 was 5000 not exactly sure what they had in mind there but OK...
I did "adjust" them all to 6850 (no headers/exhaust so it kind of flats out when you get it up past that high right now anyway) and I also bumped the shift pressures up across the board.
If you can adjust yours you would likely want to lower the MPH of the shift points to avoid deceleration down shifts from getting you squirrely heading into corners, and also think about the WOT shift points and pressures to again avoid breaking traction to keep the power to the ground.
Just curious but have you weighed your car since you did all of your mods? How much did it change your front/rear weight distribution?
The SCT tuner doesn't allow you to mess with any values in the tune. I don't know if that's because of the tuner itself, or the tune being locked somehow.
I'm going to manually shift, so the "automatic" part of the equation is off the table. Weight distribution is (or should be right around stock values. I still have to relocate the battery (I have the parts for that, it's just been too freakin' hot to work on the car).
I might also be adding a trailer hitch (so I can build myself a tire trailer), so that will add about 30 pounds to the back of the car.
I sent Bama a question about an auto-cross-specific tune. I don't expect an answer before tomorrow afternoon.