i have a 07 gt with the 4.6l 3v. one good thing about the new three valve is it has a aluminum block so its lighter then the old ones.
mpsautosalavage.com specialize mustangs. they have a mach1 engine and trans for 6500 to give you a idea. there is alot of upgrades for the new engine and 550t hp with bolt ons is common. my only complaint about the new 4.6 is i think the rev limiter is set to low because when she really starts to pull hard, if you dont watch the tach you will hit the rev limiter while the engine is still pulling. hope some of this helps but check out the web site above and they can answer your questions because they have done a bunch of swaps and can give you all the info and parts you'll need.
and if it helps i want to put the 03-04 supercharged motor and 6 spd in my 68 fastback one day!!! but for now my wife says i must stick with my built 351w lol