I'm getting about 20 mpg in around town driving and have hit 29 mpg on the highway in my 01 Cobra with stock rear gears. Depending on the mods you have your mileage will vary. I've never driven a 99-04 GT so I can't comment on whether they are more comfortable. Based on what I've read on other forums however, the 01 - 04 Cobras have the best seats of all of the fox/new edge cars.
i've been getting about 18 mpg since i got it a few months ago, but i almost never go anywhere on the interstate and i dont exactly take it easy on the right pedal.