Um.... I'm not sure. You mean the choke operation? The choke is odd. It actually PLUGS a hole in the carb when the bike is warm and the choke is OFF. When you turn the choke ON, it opens a passage to add extra fuel.
I've checked that circuit multiple times as well and checked the depth of the plungers. Everything is spot on.
I pulled the carbs a second time this morning. Pulled every possible jet on that carb AND the diaphragm. Cleaned every single passage with carb cleaner, guitar string, compressed air, etc. Soaked the slow jet, main jet and emulsion tube in Seafoam and cleaned them again. At this point, I am very, very confident that everything is clean.
Checked valve adjustment on that cylinder again. Had a "tight" .004 on the intake so re-adjusted them. The exhaust, which is a bit difficult to get to, was a loose .004 (call it a tight .005), so I left it alone. Turned the engine over and watched valve actuation. Swapped spark plugs around again.
Started it up (starts instantly, BTW) and....same thing. It's simply not running on the rear cylinder at idle. At this point, I'm starting to suspect the ignitor. I'm getting good spark when grounding a plug, but who knows what's happening in that cylinder under compression? I was texting a buddy who owns a motorcycle repair shop and he says he's seen faulty ignitors cause similar issues. It may be firing, but not at the right time, or not under the compression of the cylinder.
That's a clue, because there is fuel on the plugs when I pull them. They're not dry, like the carb isn't working. BUT....that cylinder will kick in under higher revs, so....who knows?
I'm really stumped at this point.
There are two ignitor boxes. I wonder if I can swap the plugs and see if the issue moves to the front cylinder?