Did you put an OEM Honda shift motor on it? What was wrong with the original one... why did you replace it?
Is the battery fairly new?
Is the MIL blinking or is the gear indicator blinking?
You'll need a decent multimeter and possibly an SCS tool to diagnose it. But before doing anything else unplug all harness connectors and clean them with an electrical parts spray. Apply dielectric grease to each connector when fitting them back together.
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