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Can you see what the requested torque at idle is? I don't know if HP Tuners will show that, but that's the indicator we used to diagnose a bad MAF on my car with the GM team at nationals last year. Their computers show it, but we don't have access to that in the civilian world.
My thought is maybe the tune doesn't request a higher torque level at idle than stock, so the extra drag from the supercharger is slowing the motor down.
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