IMO it seems to me that one of the "issues" that you are overlooking is the need for a Mustang specific intake manifold along with the other "associated" parts.
Here's one idea that may help you to get around the need for a Mustang intake manifold. Especially since you would like to supercharge anyway. Kill two birds with one stone!
http://kennebell.net/products/super...stang-cobra/mustang-cobra-46-liter-1996-1998/
Don't loose site of the fact that you are building a 4V DOHC that's NOT a real Cobra bottom end. This should be factored in when considering the boost levels to shoot for. IMO they should be minimal to keep your project together.
I have to agree that a better bank for the buck is to supercharge to motor that you already own. With the correct kit you could be driving your project after a weekend's work instead of gathering parts for year(s) and thinking about it.