Does partial choke application help?
I''ve tried that before, and I couldn't see any improvement
This would be an indication that you are already too rich, if choke does not make an improvement at low speed.
Have you turned your air bleed screws IN?
I believe you mean the idle mixture screws? And yes, I have adjusted those, but I am running at the stock setting now.
We are talking about the same thing, I think. Pre-77 carbs had air bleeds to change the idle mixture. While the later carbs had idle mixtures screws to change fuel meterings. For you carbs leaning the idle mixture calls for turning them out. Pod filters change the pressure in the carb venturi's, which is what pulls the fuel out of the various jets in the carb. Factory settings are unlikely to apply to your bike. If your pods are less restrictive, you will have to turn your idle air bleeds IN. If your pods are more restrictive, you will likely have to turn your Air bleeds OUT.
Fuel starvation ought to make the spark plugs read white?
They are not white, but I have not done a plug chop.
I've seen your video (more about this later), you don't have a fuel starvation issue. At least not at the speeds you are running.
What are your plug part numbers?
These are the stock NGK plugs from the local Honda dealership. I can't image plug numbers would have this siginificant of an effect. I can see this being a factor fine tuning the engine. I am tempted to strap a video camera on the bike so you can hear the effect of snapping the throttle open. 
If you are running rich, a hotter plug can help burn away the extra fuel deposits. D7EA would be a hotter plug.
I also asked in order to find out if you are running resistor plugs, which would diminish the spark voltage. If you have borderline spark, it could work okay until the cylinder pressures increased with power/ load demands. Then the compression environment would change so that spark voltage wouldn't be high enough to ionize the gasses between the electrodes. Or, no spark when you ask for power. Not sure this is your problem. But, the theory fits.
Is the rude noise coming from the exhaust or intake?
exhaust, with occasional spitting through pod filters (which is a typical lean condition)
Exhaust noise is possibly fuel buildup, then explosion when hot enough. A charge not fired, then exhausted into the muffler, then a few cycles later hot exhaust gasses make it explode, (fart).
Intake popping can be a lean mix, early spark timing, or a leaky intake valve.
I would llike to make clear that the bike runs good at small throttle openings, even at high rpm, just when I really get on the throttle, more than 1/4 throttle or so.
Kudos to you for the video! Pity you couldn't get the throttle position in view, too. 'twould almost be like being there, 'cept for the constant 1 G.
I've listen to your video, it sounds like you have a dead cylinder, as it is not running smooth, at all , at low RPM, and partial throttle. I'd check for a carbon fouled plug, given it's history. But, first I would let it idle and check the head pipe temps to find the dead cylinder and the cold pipe. Bench synced carbs should be nearly equal firing off idle setting. Your tach needle jumps around WAY too much below below 2K. (Are there tight bends in your tach cable?) Or, misfiring, due to mixture or spark problems. I really wonder if the pilot jets (and passageways) in each carb are clear and flowing.
Shame you don't have a hill nearby to load the engine at low RPM.
