I don't think that he's done anything so radical that the combination is a complete mismatch. From my take, OP is complaining on lack of bottom end throttle responsiveness (friction) until 3000 RPM, when everything gets good. The fact that the intake and heads are rpm range rated from 1500-5500 RPM, he should not be experiencing any loss of bottom end. I think something is wrong other than combination.
Am I the only guy that just doesn't read the last post before responding?