Sorry I'm late to the party. I've read this entire thread and assuming (yes I know it's not good) that the shop checked the head for cracks and found nothing, yes I get Jerry's point of internal cracks, I'd like to ask a few questions about your dual carb setup since you said it runs better when one carb is blocked.
I saw where you said you have both chokes hooked up. All of the single barrel-dual carb setups I've ever done I hooked up one choke (the rear carb). Have you checked to see if both chokes operate correctly?
Also how do you have you vacuum lines setup? I just use one, on the front carb to go to the vacuum advance.
Finally, we're both carbs rebuilt together? Meaning they have the EXACT same jets?