RE: Supercharger...
You're right there. The Mark VIII and 96-98 cobra heads are different than the newer 4V heads at the intake. The 99+ cobra 4Vs have tumble ports, and no IMRCs, plus the intake and maybe even the exhaust ports are diffent shapes.
The absolute best combination would be 03-04 cobra heads and intake on a built Mark VIII or 96-98 cobra block (forged pistons, rods, billet oil pump gears and trigger wheel, ARP hardware, etc.).
You get the light weight and strength of the aluminum "mountain" block, plus the top end with built in intercooler of the new cobra.
Put a Kenne Bell twin screw on this combo, and you can easily be in the 500-600 HP range, on pump gas.
This would take a lot of $$$. In addition to the head and intake swap, it would require swapping the entire front of the block (timing cover, chains, tensioners, accessories, etc.), plus some electronic changes to control the intercooler. Also some major fuel system changes when you decide whether to go "returnless" or not.
I'd love to that, but right now I'm going to use the stock Mark VIII engine, cobra intake, and get as much as I can out of it with a good tune.