You'll get past that 500HP pretty easy with a modern FE - but by 6000 RPM or less. I sell Scat rotating kits, as does Keith, and George, and others...
Your bottom end will be plenty strong at that power level with any cast crank - whether stock, or the Scat 4.125 or 4.250 strokers - I personally like big motors (hint..). I would recommend using a set of new H beam rods 'cuz the old stuff is "old". I use Diamond pistons in my FE stuff - - good parts, wide selection, fast service. I'd target compression between 9.8 and 10.2. Some port work on the Ed heads is near mandatory - they're pretty tame (I'm being nice) as delivered. The Comp valvetrain is a Dove setup - - decent parts - - I'd also take a look at the Erson deal. You'll need one of these rocker setups to run a solid cam - I'd like a solid in that kind of car.
For the Mustang/Shelby header questions you really need to visit the FE forum guys at :
http://www.network54.com/Forum/74182/
I'm sure a bunch of other folks will chime in shortly...
Lotsa experience on headers there...you can tell by the battered knuckles..
Barry R.
Survival Motorsports