I guess my problem is all related to fuel level issue(s). Got home last night and there was a puddle of fuel under the bike. ...
... What gets me is that the problem is intermittent. The bike ran great Monday afternoon. Yesterday, it didn't want to idle when I first cranked it. Full choke, half choke, no choke...made no difference. The idle problem is different, too. At one stop, it may hang at 2-3K rpm, the next stop, it's fine. The next it will hang a little high but then drop to normal idle.
Fuel contamination can cause this with particles intermittently catching between the float needle and seat.
This is the #3 carb. See the corrosion on the jet holder? The o-ring is past that, but could this be an issue?
It looks like the oring is past the corrosion. But, the corrosion left a sharp edge to cut the oring. A nicked oring may not seal. Check the oring for deformity.
The parts jets are marked with a slanted star looking emblem and "40".
The "slanted star" is a Keihin symbol. That's the company who made the carbs for Honda, and what is normally found in the stock carbs.
What do you make of this? What difference would the length of the body and the lay out of the holes make? Which ones would you use?
Well, you previously told us that all the parts except the mains were stock Honda. And now we see that was not the case. So now I question what other parts in the carbs aren't Honda supplied, as well. In particular, the emulsion tubes and slide needles.
The jet length determines how deep into the fuel supply the tube reaches. The shorter tubes will "starve" at a higher fuel level than the long ones that Keihin intended to be used.
The cross hole's size and number control the amount of air premixed with the fuel before passage to the carb throat. Those holes are interactive with the air screw setting. It's no wonder your previous air screw manipulation didn't behave as expected.
I'd use the jets from Keihin.
Cheers,