This is nothing new guys.
Compound Boost 2003 Mustang Cobra Twin-Turbo - Muscle Mustangs & Fast Fords Magazine

I wanted to do it when the car was mine but I didn't have the money and the tuning capability was not there.
I think that is gonna be your biggest problem. The factory fuel system will not support more than 400hp. You will probally need some sort of piggy back and larger injectors, unless there is something better out now?

You could possibly have the stock crank pulley machined down a bit to reduce your boost on the SC/ decrease parasitic loss and let the turbo do most of the work.
Another idea I had was to put a window switch on the supercharger clutch so it cuts out once the turbo spools. It might have to work a little harder to push air past the idle fins of the charger, but if the car can do it NA while cruising from the factory I'm sure some pressurized are can do the same.
Good luck!