Yes, the GT's have 8.8 Traction-lok (aka limited slip) rear ends.
The brakes between the GT and V6 are identical.
The housing side changed from 98 to 99. This is because Ford went to a wider stance in the 99+ Mustang so the housing was increased 1.25" in width. That means if you have a 99+ Mustang, you should use a 99-04 8.8 rear end.
The brakes between the GT and V6 are identical. No differences at all.
The GT 8.8 will bolt up to a V6 using the stock lower and upper control arms. The only difference is the 8.8 has quad shocks while the V6 Mustang does not have the body mounts for them. You'll have to find a wrecked GT, cut the quad shock mounts off and weld them to your body in order to use them.
You don't need the quads per say, but you may get wheel-hop without them. Despite what is popularly said on the internet, aftermarket control arms don't always cure wheel hop.
Also, you should look into installing a Gt rear sway bar....even with a stock V6 rear. The bean-counters at ford left it off to save some $$$