It depends on what kind of driving your doing, Is it a daily driver? Or weekend racer? I use stock pads on my GT I recently upgraded to Bullitt brakes though.
if all you need are pads just do the pads.. if you need rotors too you might as well go for an upgrade in the process and get the bullitt/cobra/mach type kits with the 13" rotors.
i just paid 440 shipped for a new front setup and labor should only be 100-150$ since it's a fast swap (no level place here to jack car safely to do it myself). compared to what ford wanted just for the stock pads/rotors installed i'll end up paying the same or less, and end up with a small but nice upgrade.
If just regular daily driving just go down to Napa or Autozone etc. If you want something better for improved braking check out Hawk Pads. http://www.hawkperformance.com/ Summit and Jegs sells 'em.