Steve,
Your primary jet size seems to be fine and I would not at all suspect your header size and 2" sidepipes to be causing the problem. Have you looked down the primary throttle bores with the engine idling to see if the fuel is properly atomizing or in fact dropping out in globules?
I'm assuming that you have your float levels correctly set and that your vacuum advance is connected to a port above the throttle plates. I'm also assuming you have checked compression in all cylinders (and it's adequate) and that your dual points are correctly mounted and set for proper dwell angle. With all that said and assumed correct, I would probably disassemble the primary fuel side of the carb and look for dirt or some kind of obstruction in any of the internal passage ways. At the very least you should attempt to blow out the passages with compressed air.
Sadly, I had a similar type problem with a 780 cfm vac secondary Holley many years ago and the only remedy in the final analysis was to swap it out for a 650 DP, which worked fine.
Good luck,
Mike
