I was in a hurry the other day when I posted, so I'll go into more detail this time. I've done quite a good bit of looking at piecing together a Cobra brake kit. Here's what I've found so far. This only applies to the front brakes.
Calipers/brackets: the calipers themselves can be found at any local auto store (O'Reilly, Advance, Auto Zone, etc.) for pretty cheap. Reman 96-98 Cobra calipers can be had for about $45 each, but you still need the brackets. None of the auto stores in my area can get the brackets, so that leaves the stealership. As of 10 minutes ago, those brackets are listed at $107 each from Ford. So that throws a big kink in the whole 'budget' idea.
However, in more recent searching, I may have found another way to get the brackets. The part number for the 96-98 Cobra front calipers, with the bracket, is 18B4654 and 18B4655. RockAuto has this part number listed at $42 plus a $50 core. If they would accept your GT calipers as a core (which I've heard they will), then that is a steal!
Pads: really up to you. OEM front pads are about $60. I've heard good thing about Hawk pads as well as Porterfield, which will be in the $60-$100 range. If you are on a super budget, look into the pads from Brakemotive on Ebay. Prices will be listed under the 'Rotors' section below.
Rotors: also up to you and how much money you want to spend. OEMs and similar replacement rotors made with mid-grade steel can be had for $175-$250. However, these will be plated somehow, most likely with zinc, and will not last forever. My current "zinc plated" rotors are less than 2 years old, and have a fair amount of rust on them. So, in the spirit of having rotors that last a little longer and look better, I found a company called DRT Sport. They have several different options to choose from as far as rotor quality goes; their economy rotors are still made of good quality steel, and can be had for $95; their better quality rotors are made from high-grade steel (same steel Powerslot, Wilwood, Stop Tech, Centric, etc. use in their high end rotors), and run you about $160. Best of all, all of their rotors are not zinc plated; they are E-coated (or powder coated) black, which I think looks better and is supposed to last longer.
Still, if you are looking for an even bigger budget kit, look at the Ebay seller Brakemotive, as I mentioned above. You can get front rotors and ceramic pads for $110. That is what I'm running right now. While the pads dust a little and sometimes make a little noise, and the rotors zinc plating is just about gone after 2 years, there is still nothing wrong with these brakes. 95% of people will be 100% satisfied with these brakes. They are absolutely great if you are on a budget.
Lastly, the braided brake lines.
J&M ones run about $60. Maximum Motorsports are about $80. Personal preference, but I'd probably get the cheaper ones.
So, when it's all said and done (and assuming you can get the calipers at the prices from RockAuto), you can piece together a budget kit for $255, or put together a kit with high quality pads and rotors for about $370, or some combination between. I'd say that's not bad at all considering the cheapest "kit" that you can get today is in the $550 range.
