" I put everything back together including a new manifold-to-head gasket and now the chuffing is gone. It started quickly and idled well. I revved it to 2000 RPM for about 30 seconds and it seemed smooth"
That tells me that the compression is OK, the valves are OK and there are no flat spots in the cam, otherwise it would be running funny all the time.
What I'm seeing here is one of three things. Either it is; 1. Time related ( that 30-second thing has popped up on here before) or it is 2. Vacuum related since it started right after Lane held it at 2K rpm for 30 seconds or so, then let it snap shut causing the manifold vacuum to peak, or it is 3. fuel delivery related to draining the line after a clogged filter and starving the carb(s).
OK, so Lane: when you removed the last head-to-manifold gasket before installing the present ones, was the old one torn in the middle between ports or intact?
"...so I went ...to take a test drive. Immediately off idle under load I could tell the problem was still there. I drove a few blocks with it running roughly to warm it up and could see that there was little if any improvement although it seems to idle just fine."
If it's idling fine, then the idle jets are not clogged. If they were, it would be stumbling badly at idle. It still sounds like fuel related, and a clogged fuel filter or insufficient flow rate come to mind, but that should effect all cylinders with random stumbling (or just plain die), unless......
If your fuel line goes first to one carb and has a "Y" Banjo fitting at that carb with another line running to the other carb, I would check the banjo fitting at that first carb - the fittings often have a small filter inside which might be full of crud or there is a blockage in the passage to the bowl. I remember that you supposedly changed fuel filters a while back - did you blow out the line between the tank/pump and filter, and again between the filter and first carb or "T"? If the carbs have banjo fittings and filters, are they clear?
I would be curious for you to try this: Let it cold soak - like until tomorrow evening - then, go out and start it and Immediately head out to see if it runs OK for the first 30+ seconds and THEN screws up or if it stumbles right away. Shift normally and bring it up to 3500 between shifts, if you can. That might tell us something about possible fuel starvation. Before you shut it down back at the house, keep it running but blip it from idle to 3-3.5K a few times, hard - Wham! Wham! Wham! then see how it idles. It should still idle OK, and it should still rev quickly but I suspect that after the first open throttle hit it will stumble on the subsequent ones.
And lastly, did you already swap out the coil?
Honestly, though.......You've been through a lot and, if I were you I would at this point give it to someone who troubleshoots this stuff for a living and let them fix it. As I stated at the beginning of this post, it's not the heads, the cam or something else expensive, but all of this shot-gunning has gotten expensive already so it's time to let someone end it.