you should upgrade your calipers, rotors, and brake lines. Thats all that is needed.
For calipers: You can spend a ton of a little. You can upgrade your front calipers to cobra calipers for 200 dollars~ I would go to www.gefracing.com
to look around (other places may be cheaper, just look there) you can see they have more than one cobra calipers for you to choose from. The rear calipers do not need to be altered, even the cobra's use the same rear caliper, they just have a bracket on them that allows for a larger rotor.
The cailpers alone dont do much of anything, its the larger rotor that really makes the difference in the base/gt VS cobra brakes. I would spend a bit here and get some Bear rotors, they are stonger and better made and will be much harder to warp. Slotted and drilled rotors are for looks only, they dont increase performance~ if you buy them you risk them not lasting long and them warping/cracking depending on driving and how they are made. I would buy the Bear calipers and be done with it, or just go OEM ford plain rotors (but have them coated to prevent rust) If you do NOT coat them they WILL rust and look like total CRAP so keep that in mind.
For brake lines you just need stainless steel lines, they are 75 bucks~ but well worth it.
Other sites to check out:
(i went here my first trip, very good quality, but OEM ford has red calipers ( www.gefracing.com
for instance) so unless you want a custom color get OEM. Get them powdercoated, just painting is ok.. but powdercoating is much much nicer.
Price to upgrade front: 225 for calipers, 120-400 for rotors (depending on type) and 75 for hoses, you dont need anything else other than some brake fluid and a friend to help you bleed the brakes.
When bleeding the brake you must be VERY careful to keep the fluid off of the caliper, it will remove paint, may not on powdercoat but dont risk it, use a vacume hose to silde over the bleeder valve and direct the fluid away.