You just need to pick up some MIL eliminators for the H-pipe to take care of the Check Engine Light. There was a post on this not too long ago; check it out to get the MIL eliminators.
The check engine light is definitely hurting your performance. Your 1/4 MPH should be higher than it is (especially in 60 degree weather). My car ran 72 MPH in the 1/8 (around 92 MPH in 1/4) with just flowmasters and K&N and 90+ temps.
Start with the eliminators before anything else, then go to the track to see the results. Lets us know how it turns out.
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1997 GT Flowmasters,K&N,3.27 gears
RedSOHC