I don't think its the manifold. As stated earlier, "Under Pressure" is running the same manifold and making 550whp on E85 with the same turbo. His car, to my experience and knowledge, is not creeping. I would double/triple check your wastegate and its installation. After boost leaks and confirmed out of the picture, (I'm confident its not the tune), next I'd check out the health of the motor. With it being rebuilt, it could also be a limiting factor if something is off.

You are definitely down on power but not too too down considering you're using pump gas and lower compression. Iron out whats causing the creep, and I'll bet you'll find your lost power.