Time to upgrade and tune:

I am trading my current 60k mile '99 GT auto (sig) for a 5k miles 5-speed 2001 GT. Here is what it has:

4:30s (4:33)
CAI
flowmaster 40 series welded in

Thats all it has as for performance. I am thinking I will go MAC O/R X or maybe something like Dr.Gas or Steeda X pipe. I then want to upgrade the shifter. I do want to do a little more (staying N/A), but what are my best options with what this car already has? Do underdrive pullies really work? Bigger TB?

I also want to get it dyno tuned and see what they can squeez out of her.
 
Pullies and gears are supposedly one of the best things you can do for the feeling of torque. If you want to squeeze out every last bit of hp, then get the TB/plenum and you might want to get 2.5" exhaust flowtubes. Cams are also something you should consider.