I was thinking some on your comments about the lack of low end power. Keep in mind that you built a rather short runner intake manifold. This alone will affect your power curve. The manifold is not short enough to not affect the curve but to short to provide low end power.

If I recall your comment of the boost being lower than it first was, did you not reduce the compression ratio? The reduced compression also makes more volume to fill. The air passing through the engine will be equal or greater than previous but the net affect with a positive displacement blower is a lower boost number. With a positive displacement blower boost is a measure of air not getting into the engine.
So with a bit more cam, some porting work and lower compression your airflow has been increased. Now you need to get the blower to give you more air.