in another post, i believe you said you ported the exhaust side of the heads. i think this has a significant effect on velocity at lower rpms, especially if you make the intake bigger. i was experimenting with the maf and tb a while ago and found that making it larger seems to tune in more power at a certain rpm band- moves it up higher or spreads it out over a wider range. like a 2 1/2 inch intake with stock tb makes the car slightly more torky down low and mids because of increased velocity at lower speeds across the maf (cooling the hot wires a little faster increases fuel and spark timing very slightly), but open the intake up to 3 1/2+ inches and throttle response goes up along with slightly more boost, but tuned in for higher velocity when in the high rpm ranges for emphasis on top end power (less emphasis on low end). In my case, my sc is pretty much stock- no major power mods except for a ported supercharger, but my car pretty much reacts like i described above.
you would probably be better off with the bigger intake and over spinning the supercharger a bit more. get the supercharger ported if you havent done it yet- you will like the sound and you will definitely feel an increase in power especially in the mids and highs.