It sounds like you got a few things going on at once here.
1. I dare not suggest anything with regard the issues you're experiencing. I'm too far removed and too inexperienced to hazzard a guess.
You're right though - Heat is the enemy and overheating could have fouled many things.
I will hazzard this guess if you'll allow - 472 stroker shelby block, in a CSX4 series, sounds like it may have been built by Gessford engines...? Maybe shoot them a call and quote the block number to see what they know.
2. For me, Cobras are all about the engine. 4x2 looks the goods under the hood!
Next best thing to an 8 stack, but without the headaches. Sure it's twice and complicated as a single carb, but it's also at least twice as nice
As for the intake, try DSC Motorsport (I went for a tunnel wedge myself, a single plane intake, but the blue thunder dual plane are very nice too).
DSC Motorsport
Or ask the boys on the FORDFE.com forum.
3. 600hp on pump gas shouldn't be hard, with the cubes you've got already.
It could even be made streetable.
If it were me, I wouldn't worry about the HP numbers. Just get an engine builder you trust and that "knows" what you are after, and have him build it.
I've a theory that suggests a 500hp dual quad, dual plane intake, cam'ed appropriately, is more than enough to spin the tires in almost every gear, almost every time you mash the pedal.
Good luck with your engine!
...and keep us posted. I love the engine (re-)build threads.