I disagree with this statement, and provide this piece of anecdotal data to serve as a blanket assumption covering all races between 99+ GTs and 96-98 Cobras...
Clicky clicky
EDIT- Well, crap. The thread is still alive but the vids are no longer being hosted so they're dead. Oh well. He smoked all three of those cars, with the most satisfying being the last because the guy red-lighted like crazy and still got pulled hard.
On a more serious note, there is at least a 20-30 rwhp difference between the most stock 96-98 Cobra and stock 99+ GT. The low end torque advantage of the GT is only going to matter if both cars are launching from idle, which would be pretty foolish. 20-30 rwhp shouldn't provide too big of an advantage (only 2-3 lengths over a full 1/4 mile) and can be overcome easily with some mods to the GT. Nevertheless, stock for stock the Cobra will come out on top assuming equal driving...