I know of a guy on another car platform that had a very similar problem - supercharged setup, in the upper revs power just dropped off for no obvious reason. Turned out a plastic section of his intake was bending shut from the pressure at the upper RPMs, closing off the intake somewhat. I doubt that's your problem, but it's another thing to look for. Sounds like it has to be some sort of mechanical problem because anything tune-related that would cause that seems like it'd be fairly obvious to the tuner.
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