A 28 spline 8.8" rearend from a 99-04 GT is your best bet. The rear brakes are the same so there's no gain there, however the rearend itself is larger and as Everett said you get the limited slip, or traction lok to be manufacturer specific.
This will get you better traction from a dig and eliminate those embarrassing one wheel burnouts
The v8 rearends also have quad shocks which can be transferred into your v6, the bolt holes are in the frame.
Unless you know the exact mileage of the car donating the rear and how it's been driven I'd plan on rebuilding the rear. Rebuild kits are available at vendors like American Muscle etc. You may also want to upgrade gears since you'll have the diff. cracked open. Keep in mind changing from the stock 3.27's and going to a taller ratio will throw your speedometer off slightly and will require calibration for it to be correct.
Finally, you can use a 94-98 8.8" rear but it will be ~.5" narrower on each side which would require hubcentric wheel spacers to push the wheels out so they don't look so tucked in.
12 Black GT500 SVT PP l 2.6 Pulley/Idler l Airaid l o/r X l 305 NT555R's l Recaros l
04 Azure Blue Mach 1 / 03 Sonic Blue 3.8 / 14 Sterling Grey F150 FX4 402A 5.0 / 11 GT500 R.I.P.