I think everybody is forgetting a very important point here. The LS1 engine(from what I hear) isn't good for more than 550-600 hp without changing the internals. The new cobra's 4.6(which isn't just a GT's with a blower), is being tested to 1000 hp with no internal modifications(gotta love Manley). Another huge point is this:
The '01 cobra could hold it's own in a straight line, and could out-corner the crap out of a Camaro/Trans-Am/Firebird. Ford went after the Z06 when they designed the '03 cobra.
Any naturally aspirated engine with the same horsepower as a blown one, will always win. But all bolt-ons done to the blown engine will have a much bigger power gain, for the exact same price.
If you had a 355spyder, and I had a civic with mods that equalled the value of your car, I would lay the smackdown on you. But in the end I still only have a civic. Think about it.