rdk - unless you have back to back dyno numbers before and after the change (under similar ambient conditions), you don't really know what you've got. Seat of the pants is a terrible indicator of actual performance. And, if it is actually weaker, it could be due to any number of other things related to the work (vacuum leaks, timing change, fuel system malfunction, etc.). Do you have the bigger egr spacer as well?
Intake manifold runner length changes can directly affect torque in different rpm ranges (in general the longer the runner the better the bottom end torque at the cost of higher rpm power). But that runner length starts at the intake plenum - which is well downstream of where you made your change. The change you made can remove a flow obstruction which might help higher rpm power levels if that were the flow bottleneck in the system. IN your case, it's not - so the change should have made little difference at all. I wouldn't lose too much sleep over it - get your intake changed/ported, and then see what you've got. IN any event - what can you do about it? Not like you're gonna put another stock one on to check and see, right?