IMO it comes down to personal taste. Someone like me would say get a 5.0 GT/ 4.6 Cobra SN95 (215 & 305hp respectivly) car because its my personal favorite, but twenty people will say i'm a fool cause a fox car is faster (205-225hp-F/I models). Sure it is, but I'm into handling and the fox cars don't compare. On the other hand 20 more people will say I'm an idiot and go get a 99+ car.
And how about the 4.6 cars, 99+ is when the 4.6 started to make more power (260hp) and the 96-98 are slightly weaker (215-225hp). They aren't a slow car, just slower than others. My sentra is a slow car!
My advice to you is to just pick your favorite platform/body style. It doesn't matter which ones faster from the factory IMO cause how many factory stangs are left?
Go thru some parts catalogues, you will see the fox cars (pre 94) have better parts availablity at lower prices, The 94-95 cars cost more to mod and are somewhat limited in options due to only 2 years of production.
If you get a fox car make sure you consider speed density vs a Mass Air (MAF) car. If you get a SN95 consider 5.0, 4.6 2V or 4.6 4V (Cobra)
How much street do you want? How much strip do you want? If you don't have a preferance to any particular model I suggest deciding what you want the car to be in the end and choose the platform to best suits your needs.
Enjoy!
LOL