Ok, the final verdict is:
The Check engine light was coming on because of an incomplete ODB test the computer would run. The old battery must have been compensating for this which is why it didn't show up until I change it, and reset the computers code. I also had damaged spark plugs and spark plug wires that were not getting the full amount of energy sent out, and that was causing the stuttering on acceleration. A couple expensive code scans later and a 'major' tune fixed the problem.
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Tuesday, July 25th, 2006 AT 8:35 AM