Aaron, it looks as if you have checked almost all the possible problem areas, just a couple I can think of. How is the carb balance? Did you balance them by ear, or with a balance tool? If by ear, was there anything different?
I had one car with a similar problem. Everything appeared OK, but still it would not idle nicely. Listening to the carb suction one was not a constant hiss, it had a flutter in the sound, like a syncopation.
I ultimately found one inlet valve was sticking, just slightly, [a few thou] open at idle. It must not have done it at higher revs & the thing ran quite well, & the valve or seat were not burnt.
The other problem giving something similar was minor flooding of the front carb. I finally found it had about 2.5 PSI fuel pressure, which was high enough to make it flood sometimes but not always.
It was worst if you were making a few stops. It would run rough at traffic lights, & take a few revs to 3 or 4 thousand RPM to come clean.
If you ran the thing, then removed the piston [with its needle] from the front carb quickly, you could see the petrol rise in the main jet, as the residual pressure in the fuel system slowly pushed the float level in the front carb too high. Sometimes fuel would well out of the jet, making the throat of the carb wet with fuel.
It is always the front carb, as the angle of the float bowl on it makes it more prone to flooding.
I had to reduce the fuel pressure to under 2 PSI to overcome the problem. Of course I reduced it to about 1.5 PSI first up, & induced fuel starvation, so it's a narrow difference between too high & too low.
If this is your problem, you could try a pressure regulator, I did but had trouble with it. I found that fitting extra gaskets made of cardboard between the pump & the block reduced the pressure. It was just a matter of how many to get just under 2 PSI.
Hasbeen
