96-98 GT = Non-PI 2 valve engine (215-225 HP, heads don't flow very well, upgrading to the "PI" heads and intake from 99-04 common)
99-04 GT = PI 2 valve engine (260 HP)
96-04 Cobra = 4 valve engine (96-98=305, 99&01=320, 03&04=390)
I've had a 99 PI engine and a 96 NPI engine. the difference is big, and if you want to get more power out of the motor you should start with a PI engine IMHO, because you'll need to make a NPI engine PI to get the most out of it.
I'm probably getting a 96 Cobra in a week or so, and from the one drive i've had in it i can say that the power delivery is much smoother in the 4 valve. the 2 valve isn't a bad engine and you can get a lot of power from it, but the powerband in the 4 valve engine is much wider.
I'd go with a PI 2 valve if you want to do a lot of work on it for less $$, but if you can get a 4 valve in good shape, go for it. If you get a 2 valve that is from 96-mid 01, make sure to check if the engine has had the coolant crossover passage (attached to the upper intake manifold) replaced.
GL man!