100% of the time on 98/04 reprogramed PCM's,you need to have a case learn done or what GM calls it is a Crankshaft Position Variation Learn Procedure .If you have an auto zone go by there and they will scan the car for free and give you the code.I bet money on the code will be a DTC P1336.Here is the procedure must be performed
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Which PCM did you buy???
~Larry~