V6's have the same brakes as GT's. And yes they are MUCH better brakes. The front brake design offers better cooling than the fox brakes even though they are the same diameter rotors and pistons.
As an upgrade, look for a set of 99-04 GT/V6 calipers on ebay for cheap. They are HUGE calipers and bolt right on with a little modification.
For parts, you need the spindles and everything attached to them. That means spindles, hubs, calipers, rotors, brake lines. I'd get a set of SS lines instead. Get them for a FOX mustang, not SN95. They work with all calipers, but the chassis designation picks what size fittings connect it to the body lines.
You'll also need the MC and booster
You back, take the rear axles out and everything bolted onto the axle ends. That's axle brackets, calipers, rotors, dust sheilds, and soft lines.
www.sn95brakes.com is a good place to start reading.