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With a 02 PCM you will need a 02 harness, unless you want to repin almost every pin in the 98 harness connectors, then there will still be some issues. It would also help to know what MY vehicke you are putting the 02 engine and PCM in.
I have seen a automatic transmission destroyed in this situation the sensors,harness and computer were not the same. Maybe check with Speartech or painless wiring.