You've done a beautiful job with this bike!
About the carbs:
since you've described that the needles in the slides need 3 shim washers to even get close to correct performance, this indicates the brass inside (at least those needles) are Keyster parts, not Keihin parts. The OEM Keihin idle jets for the PD42B series carbs was/is #35, and the mainjets were #105 if the bike was sold in California or New York/New Jersey or #110 if outside there.
If the jets are Keyster jets, they would require the numbers be #38 idle and #115/#120 respectively. This would help to drop the choke sooner while warming up.
Also: today's gasolines burn MUCH too slowly when compared with the 1978 fuels the bike was designed to drink. Our modern Regular grade burns at about the same speed as the 1970s era Premiums did, so try using Regular gas to see if it settles down sooner after cold start, and it should also run cooler. When the fuel is still burning as it exits the head (i.e. too much octane in today's numbers) it puts a lot more heat into the front of the engine, which slowly transfers throughout.
Also: if the idle jets are Keyster jets, then the adjustment range of 1.5 to 2.5 turns of the low-speed mix screw will end up being turned further out to get enough fuel to let it run well at idle when hot.