What most often causes this on the 46C carbs is mis-alignment (or bent part) in the coupler that joins the 1-2 carbs' choke rod to the 3-4 side's choke rod. I have rebuilt/cleaned a number of them and ended up with the same situation yours has now, and found that diassembling and reassembling that "junction" between them made the correction.
Short of having some pictures to try to point out the "why" of it, if you'll look closely at that coupler gizmo, you'll probably find that it just wasn't aligned right on reassembly at some point. I use a thin wire, wrapped 270 degrees around the coupler, to pull the 1-2 rod to the right position before meshing the left- and right-hand sides together before putting them in the rack again. Sometimes I have found where someone before me actually bent the thin sheet metal plate of that coupler, which then wouldn't let them mesh up correctly. It has always been a mis-assembly problem on all of the 46C carbs (and the similar ones on the 750 bikes) when I have seen this issue.
The 500/550C is very cold-blooded, due to the PD46C calibration. There are 2 pilot jet (idle circuit) holes toward the front of the carbs, one is directly above the [pressed-in] pilot [idle] jet and the other is downstream of the slide, directly above the idle-mix screw. Most of the time, the tiny O-rings in this idle-mix screw are now dried out and won't seal, which lets too much air in below the slide, making idle almost impossible. Renewiing those tiny O-ring and clearing the hole into the throat with a thin wire fixes it up: you'll have to [heat up the body and] pull out the idle jet to get to its hole into the throat, so be gentle with those pressed-in idle jets.
There is a tiny washer above that idle-mix screw, too, which is used to squish the O-ring. Make sure it is still there?
Update:
And, lest I forget - the PD46C carbs are jetted differently from the PD46A/B: the "C" idle jet is #42, the mainjet is #95 (unless you're in Europe, where it might be #78 instead) and the float level is 12.5mm deep. I have also seen #90 mainjets in the PD46C, but don't know if they were factory original.
(The float depth in PC46A is 14.5mm, in B & C it is 12.5mm).
The PD46C needles should be in clip slot #2 (2nd from blunt end) and the idle airscrew is set at 1.5 turns, +/-1/4 turn there.