What ebay kits do you speak of? Caliper upgrades? Or just the bling drilled rotors?
Take it from me, stock 99+ GT twin piston PBR calipers are all you'll ever need on the street. If you want to fill out the wheels a little, upgrade to the Cobra setup, but do both front and rear, and change the MC as well for correct proportion/bias. Your V6 spindles are fully compatible with the GT or Cobra setups. You will only need to change calipers and caliper brackets, and rotors if you go with the 13" Cobra stuff. Rear axle/caliper brackets will need changed to go Cobra as well.
If you want even further than that, you can get kits for Brembo, BAER, StopTech, Wilwood, and other kits for front and rear brakes. All spindles from 94-04 will be compatible with the kits.
I have a thread for 13" brake options, including my Wilwood setup.
http://sn95forums.com/showthread.php?56682-front-13-quot-brake-Caliper-options