Big question. The Supercharged V6 didn't come out until 1992, so how does an 89 get blown?
The 94 intake will cause PCM problems unless you get an AFC controller, but otherwise, if the engine is from an 89, get the pcm from the donor car (actually it'* an ECM, which will help, as you have a manual trans, and don't want the automatic axle crap in the pcm anyway).
If it'* actually supercharged, what car did you REALLY get it out of?
for more information.
Moving this to Performance.