Have you looked at the plugs when you pull them? Try idling it for a while under the condition where it sounds bad. Then pull the plugs and see what they look like. You'll be able to tell if it's one cylinder, one bank, all lean, or all rich. That will give you a better idea what to look for.

You can also try swaping carbs and/or ignition if one engine is running good. See if it follows one particular component.

I'm gonna go in an opposite direction here. It sounds lean to me... Pull the flame arrestor off and look down the venturi's to verify proper operation. I've found that shift stalls are usually from being lean on holley's. If the carb is dumping you'll know it at idle. I'd try backing out the mixture screws little by little and see how it effects the idle/shift. Lots of other things to check but I'd probably start with that.

Also, do a visual inspection to be sure all the rubber vacuum plugs are in place and not rotted/cracked, that will also do it.