you said in one post that you rechecked the accelerator pump clearance?
This is where i would look again there is a lot of misleading info on how to properly adjust the accelerator pump lever adjustment out there.
By reading and listening to what you are saying is the motor is hesitating when you quickly open the throttle Right?
Ok that is most often due to insufficient amount of accelerator pump shot or not quick enough shot .
Does the accelerator pump squirt like popping a zit or does it dribble when you barely move the throttle lever?
I have had this problem before on many holley's because people read the Holley tune ing books and always try and adjust the lever to have .015 clearance between the pump lever and the spring bolt at WOT
This is where i think the problem comes from .
The way i adjust the pump is like this i take the cam off and see
how well the pump squirts with me moving the lever with my finger also i watch very closely how far up the lever returns when the pump is at rest.
Then i make the spring bolt adjustment so the bolt is very short.
then install the cam in the original factory position.
Now the lever and pump arm should be very loose and this is where you need to be to start.
Now slowly and very carefully start to lengthen the bolt adjustment
so it just barely touched the pump lever at it resting position! This is the most important part! the adjustment should be so that the pump is getting full stroke!
You do not know how many holley's i have fixed with this simple adjustment if the pump is getting full stroke i bet your problem will go away .
Cj