Sorry, but the 03 Cobra block has forged internals, an iron block, and is flat-out race-ready. Don't think it could handle over 600hp? You're very much wrong on that one.
http://www.modularfords.com/forums/showthread.php?s=&threadid=1069
697hp, motor runs fine. This isn't the only instance of somebody pushing well over 600hp from the new motor. It's solid as they come from the factory.
The Supra block is known to handle upwards of 700hp fine. It's a good block, though if I were going for a Japanese engine, I'd get a Skyline motor instead -- more low-end torque and will handle more power. I just notice that a lot of people think the 2JZ-GTE is indestructable, but it certainly isn't.
I don't want to get into an argument over cars, but I still would rather have the Supra over a mustang. Supras ARE bad off the line. Why? Because of the frickin' huge turbos people run. 700-1000 HP is gonna get you nothing but wheelspin, especially on an IRS suspension w/o Anti-Squat.
Now wait -- you say traction is the problem.. How is that any different from what the 03 Cobra would suffer from? Yes, the 03 has IRS, but so far is handling the ~700hp that NitrousPete (see above link) is running through it. A lot of the high-power Supras are running Ford 9" rears.
Why do 500hp (modded) 03 Cobras, in the hands of capable drivers, run 10's when not suffering from traction problems? Why do 500hp (modded) Supras, in the hands of capable drivers, run 11's when not suffering from traction problems?
Because of the turbo lag. The Cobra doesn't have that problem, due to the roots-type blower (or, in the case of the Kenne Bell, a twin-screw design). The torque curve of the 03 Corba is something that no Supra I've seen can match. Check out the usual Supra Forums and do a search for 03 Cobra -- see that they give it credit for being a great car.
I don't hate the Supra, I just don't like it. If that's your thing, then good for you. I'd just much rather drive an American car, and one that can produce lots of low-end torque. The 1/4 mile is all about low-end power, which is why muscle cars are so dominant. Sure, once that turbo is spooled up in the Supra, it will accelerate nice (as evidenced by the high trap speeds of Supras), but off the line, they just don't have the balls to compete.