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I'm sort of just thinking out loud here, but the big difference between the N51 & N52 is the N51 has a three stage intake manifold and a secondary air pump. So does your motor have the 3SIM on it, and does it have the air pump installed?
If yes and yes, then I don't think you need to mess with the ECU, there is something else causing the problems. If no to either of those, then maybe it would be easier to just re-install those N51 components?
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