I'm pretty sure my stock times for an STi are within the top ten in the country. Not bragging, just stating what I think is the truth.
NOW...in my experience with stock 03 Cobras (the other years are no competition in stock form), I am 1 for 3. The only reason I won the 1 race was due to excessive spin by the Cobra driver off the line.
The other 2 races I had the lead until well past the 1/8th mile, and then got passed quite easily. If it had continued, I would be embarrassing.
As others have stated, in their element, these 2 cars are probably at the top of the heap. Talking mod for mod potential and once again you need to consider their element. Don't forget that mods also include suspension work, and if you go mod for mod in that direction, can you honestly say a Cobra is better? Nope. Converseley, for outright raping speed, the Cobra mod for mod path dwarfs the STi. Probably on the order of for every 1 dollar spend on the Cobra, you'll need at least 3 (and some big kahunas) to match it in the STi, and thats probably conservative.
Total respect to both platforms. I for one am happy to see domestics finally start stepping up to the plate. The Z06 and Cobra are both great examples of how a car should be built for the intended purpose.
I cross shopped the Cobra against the STi, and chose the STi for it's AWD capabiblity, my love for the all-around platform, and to be honest, the shifting action in the Cobra just felt attrocious...like a truck. But it did ride smoother!!