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I take it that the JDM alternator was not playing nice with the ECU? I'd be curious to see if a USDM alternator will fix your battery light issue. I have a JDM BP6D that i'm getting ready to drop in. Maybe there is something different about the JDM alternator
Swapping back to the USDM alternator fixed it, not sure if there's a wiring difference or this alternator was just bad. The JDM one was only charging at ~12.05v. I've been on the lookout for a JDM ECU as a stopgap before I invest in a MS, but they seem pretty thin on the ground.