If those holes aren't plugged then you have a vacuum leak on each cylinder. For sure would cause dieing at low revs. You could have other issues but these vacuum leaks aren't helping.
Seems like those are 5 mm but I’m not sure. I’d suggest getting a few size threads from a hardware store to test.
The plugs need to be just long enough to bottom out
True, I had a shorted spark plug once. Iridium. Looked clean but no spark out of it. That was after messing with mixtures and probably a lot of idling. New plugs made a big improvement.
Seems like problem could be with the choke system itself. Maybe the one carb is being choked more which would make it get more fuel which makes it run cooler?
Be careful what you run through the carbs, I think Seafoam is about the only "safe" cleaner to run through the carbs besides running a few ounces of ATF in the gas. Seafoam at it's recommended dosage only.