a good place to start would be to get a Bonneville SSEi and put all the drivetrain and suspension under it.
if you already have the supercharged engine, then you're only gonna want the suspension goodies out of the Bonneville.
after that, get a free breathing exhaust and gut the stock air box- once you take the filter out you will see what needs to go. they put a HUGE filter element in there and then make it breathe thru a tiny little hole to keep it nice and quiet. hell, do the airbox right now because it's free and only takes a little bit of time.
i don't know if anyone makes a program like LS1edit to tune that engine family, but if you want to ditch the stock ecm and convert to a Megasquirt setup you can tune that on the fly with a Droid smart phone or tablet now with a free app and usb cable...