Sounds like an issue with the tune or a mechanical problem.
Is it tuned? Do you run an FMU or do actually have a good 1:1 rising rate regulator on the car? Although I am sure it is different with each tuner; mine requested 39# fuel pressure; and I only run 10degrees advance as the rest is ECM managed.
With a more restrictive intake, the car should actually feel MORE snappy in theory. Although I'm really not sure how much HP is lost between intake design once boost is added; I currenly run a Performer 5.0( not even the RPMII) with 165cc heads on my strim. It is the 8-10psi setup making 11psi with a powerpipe. The response in 2nd gear is instant and violent. It will just flash the tach as it spins the tires as hard as possible hooked up from a 45 roll.
I believe this is a combination of forced induction and smaller valves/runners creating tremendous intake velocity. The added cubes alone of a 331 should be getting things done in a hurry. I believe something is amis and not just a 'mismatch' on the combo.