a lot of write ups on how to. very easy if you are mechanically inclined at all.
here is one site where i got a lot of my info
87-93* Ford Fox Body Mustang Brake Upgrades
and here is what you were looking for from that site.
The '94-98 cars rear axle shafts are .75" longer than the stock axles on the '87-93 cars. Be sure you note this longer axle if you are running 9" wide wheels because you will need the wheels with the extra offset like the M179 Ford '95 Cobra Rs (6.45" 36mm) -- which are now discontinued! You can use the 8" wide wheels without issue, but if you want 9" wide wheels you need to convert the brakes to use the stock rear track with Ranger axle shafts!
The V6 cars use the 7.5" rear axle. So the axle housing and gears will be no good to the 8.8" rear end, but everything else will! The '94-98 GT and Cobras use the 8.8 rear end with a 3.27 gear in them stock. Most yards will only sell the complete rear axle assembly presently. So if you get the 8.8 unit, just bolt that in. It will be a direct swap except the brake line fittings to the chassis will need to be adapted. You can also use the stock drum brake hardlines with 2 adapters at the caliper softlines to convert.
Remember that the V6/GT/Cobra all use the same axles, calipers, and brake lines. The axle bracket, rotors and pads (same pads as the V6/GT, just thinner) are specific to the Cobra.