Go to JY, pull the SN95 spindles and whatever other parts yourself, then order a set of new PBR calipers and brackets from wherever (rockauto has them) for the fronts. For the rears you'll need to do caliper mount brackets when you pull the axles for the 5 lugs plus the cobra caliper brackets and you can use any 94-04 rear calipers since they are all the same.
Figure you'll spend $300 shipped for a good quality new Cobra rotor/pad setup. Another $40-$50 for good used rear calipers, $50 for rear Cobra caliper brackets, $150 for the caliper bracket rear mounts, $250-$300 for Cobra front calipers and brackets, plus the cost of whatever you pull from the JY like the spindles/lines/rear axles etc... Its not cheap, $1400 is a little more expensive than I've seen some done for but its not the most expensive I've seen either.
A much cheaper and still effective setup is to do a 99-04 GT brake setup. They had dual pistons calipers up front but not the big rotors the Cobras had. They still stop LIGHT YEARS better than the fox setup and even the 94-98 GT setup.
2000 Mustang GT Steeda #0048 34k miles. 99 Cobra 4V swapped, FTBR IRS swapped, exhaust, tuned by James Gordon.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.