I drove the 03 Cobra and the base Vette (not Z06) in Phoenix back-to-back in comparison in April at Bondurant. There is a $15K price difference in the base Vette and the Cobra Coupe. I had never driven a Vette, and practically never really driven a Cobra hard, but I thought the Vette would handle heads and shoulders above the Cobra, especially on a road course. I was pleasantly surprised that the Cobra more than held its own - it handled great as well! The Vette had HUD and a couple of other trivial extras, but GM always tries to throw gimmicks in with their cars. As far as fit and finish, maybe some parts of the Vette are put together better, but your tolerances (ie body gaps and such) can only be so good with a chopped fiberglass body. Bottom line is that although the Vette has a truer sports car look, I'd take the Cobra with it's SVT tuned suspension and bact seat, then put the $15K towards a Focus SVT as my daily driver.
Seth