Are you designing VGT superchargers from the ground up, or using off-the-shelf?
One thing to point out here, Koenigsegg started using off the shelf-technology for his grounds-up supercar... as do most manufacturers who don't have a big budget.
If you're really serious about making this all work, I suggest reading this:
http://dpcars.net
As the site has basically a full build diary of what the guy did to build his own track car.
It's certainly not a supercar, but it's a hayabusa powered (soon to be powered by a V8-engine based on the Busa, built by another company) four-wheel drive trackster, with a full tub, CF body, completely custom suspension and differentials.
The amount of work that goes into a project this small is mind-boggling, to say the least. But read through it, and you'll get some ideas on what other programs besides CAD you'd need for the designing process, programs for calculating loads, parts strength, aerodynamics, etcetera... that's not to mention the software you'd need for modelling the engine and the stresses involved in designing the reciprocating assembly. Which this guy skipped by buying an engine (albeit an experimental one) off-the-shelf.
One thing to note: you can't just fuse two straight-sixes at the crank. You also have to redesign the head of one of the siamesed engines... swap around the intake and exhaust ports (lucky you if you can just turn the head around on the block) and design custom cams (ground from fresh billet) to run the valves (as the timing will be completely different with the head turned around). Simpler, maybe, to install the block backwards, but you'd still have to grind new cams to work the valves in reverse order... or something.
Of course, you could short-cut it and do it the way other "supercar-challenger" builders do it. Build a basic, crude, tube-frame racer, cover it in an exotic-looking fiberglass shell, stick a big V8 with turbos in the back and call it a day, but you will likely want to do it the way this guy did it.