Note- it was just in 5.0 Mag this month that a '03 GT ran a 13.8x in stock trim, stock tires and all.
A '99 Cobra and a '03 GT will cost the same so that is out the window. The '99 Cobra will have better resale value in a few yrs. GT's depresiate quick as Cobra's seem to level off.
Stock for stock the time will be about the same in the 1/4 with a slight edge going to the GT.
Mods are a cheeper on a GT but you get less hp out of them. It is a lot easier to make some big hp out of a 4v then it is a 2v.