What you heard about the 99 Cobra, in stock trim is true. They under-performed. But with a few quick addons, you can get it running pretty damn good. The roush is more of an overall package. A little better performance than the GT with much better handiling, and a different appearance package (un-supercharged of coarse).
If I was in your shoes, I would go with the 99 Cobra and work on it. A cold air kit and open up the exhaust will cost less than $500 and create a good difference.
As for making a GT as fast as a Cobra pretty cheaply, there is no such animal. Take whatever you would do to the GT and do half of that to the Cobra, and it will smoke the more heavily modified GT. Trust me, I wish I would have bought a Cobra instead of a GT. Too late now, I got too much $ in the GT to get out of it without losing my azz. Hey, wanna buy a low 13 second GT
for under 20K? Only 25k miles on it and the motor only has 3K.
SERIOUSLY! If you are interested, I will email you a list of the things done to it, and send a pic.