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I see you have not been attended to as yet, apologies from justanswer.
Did you have the PCM reflashed after the supercharger installation?
How many miles on this engine now?
Did you look at your intake valves during the manifold swap?
Did they look clean or carboned up?
If the engine is healthy, then you need to talk to the supplier.
It may need to go onto a dyno, for remapping while observing A/F ratio data.