is there a difference between 93 r33 gts-t and 96 series2 gts-t engines and what one would be best to upgrade they have similar k's

no difference in the actual engine.

Depends how you define "engine" :p The ignition system is different, as is the throttle position sensor and a bunch of little bits like that. The turbo is also different, with a nylon comressor wheel. The computer is different too - at least, I'm led to believe you can't substitute one for the other (probably because of the different sensors and ignition system, I guess).