There are a few options to make the transmission perform better.
1. SuperChip (around $225, and piece of cake to install) This helps the PCM control the tranny better. Firmer shifts, and very good torque converter locking.
2. TransGo shift kit. $38, a little more work to install, but the shifts become more accurate, and firmer. Less wear on the tranny since the transition period between gears is shorter. Would be GREAT with a Superchip.
3. Level Ten PTS tranny kit. It's around $500-600+ labor, very intensive tranny overhaul. Suggest getting a used one from junkyard, and sending it to them to rebuild. Then, once they have done their magic with that tranny, swap it with yours. The end result is a bullet-proof ATX that should be able to handle tons of power.
I already have the SuperChip. After the turbo install, I will be looking at the complete LevelTen rebuild. Then I can bump up the boost

Hope that helps.