I don't race on a dyno, so that doesn't help. Bolting on heads that flow 20-40cfm better should pick up a few .10. So that is a little out of the ordinary.
The thing is that more head flow doesn't necessarily equal better performance with all things being the same. The car runs less MPH than before so its likely that changing the heads probably have some negative effect on the power band OR the RPMs are too high with the 4.56 gears.
If you lost port velocity or compression, you may have lost some torque in the lower part of your powerband. It could also be that the tune is less ideal than before.
I mention the dyno results because the thing makes power literally everywhere between 3000 and 6200 rpm, which is likely the range you're running in all the time as well. If you had a really big cam and some super high flow heads (300+) maybe a single plane intake might be more fitting.