First: the bike looks to be in GREAT shape! I don't see those in that nice condition very often.

About the fuel delivery: check that in all of the off-on trips for the carbs that the fuel hose still drains DOWN all the way to the carb's fuel rail. If it goes down, then back up, then down again, it can actually pump hot air back against the meager fuel head pressure when the engine warms up the carbs, pushing the fuel back up into the petcock. It looks like a bubble happening if you get to see it, but it's REAL quick-moving and only visible with clear fuel lines (which usually leak, because they are not the right diameter for these pipes). I recently had to remove an inline fuel filter from a 1979 CB650 because it went horizontal on the way between the tank and carbs, and as soon as it got warm it would hydraulically lock the fuel line unless the bike was tilted toward the right (a lot), then it would 'burp' the bubble and run OK until it was parked and the fuel line went dry again (then it repeated the cycle). The bike would run about 8 minutes or 1.5 miles thru the neighborhood each time before it would die from a cold startup.
In the CV-type piston carbs, if the slide hangs up ANYWHERE in its travel, that MUST be freed up. Sometimes the cover of the carb warps a bit, and the tiny (VERY tiny) clearance between the cover and the fast-moving slide causes 'stiction': they must be completely free, clean, and clear of any debris. If not, that piston will stick in the 'tight' spot, whether it is up high or down low, and that cylinder will suffer. If it sticks HIGH then that one will be rich, if LOW then that one will be lean. Most of the time I have seen them stick HIGH. This also makes the bike hard to start when hot. When it cools off the CV piston shrinks and drops back down, then the engine starts better, and the cycle repeats.
The warpage that can happen to the CV carbs' cover is purely due to the type of metals used at the time: Honda didn't think these bikes would be here now, so it isn't the finest aluminum alloy. If you can determine for sure which cylinder is suffering the stuck piston, remove that cover and try polishing the inside of it with a jeweler's rouge like Simichrome: you will find the "high" spot as the area that looks different from the rest of the inside. This rouge won't alter the tiny piston clearance required while you do this, but can point out that spot(s) that needs to be 'pushed back' a tiny bit for smooth operation of the piston.
Now, about the engine: in your 'top end rebuild' did you replace the piston rings only, or did you have the cylinders bored and new pistons & rings installed, and with a piston clearance of LESS than 0.001"? It must be that tight. I use 0.0008" maximum. If they are more than 0.0015" then it will not seat the new rings enough to ever stop smoking: have seen this too many times.

If you just honed it and replaced the rings, they will not seal again. Ever. Nature of the SOHC4 engine. They may get close to sealing, but they will not seal because the bores are not round anymore after about 8k miles, but the outer 2 are egg-shaped while the inner 2 look sort of like a cam lobe with the narrow part being the original diameter and the wide part nearest the cam chain tunnel. The metals are now cured: this means that boring them an oversize WILL ensure forever-round bores, and they won't shift again. But, they MUST be bored for a TIGHT clearance, and the top of the cylinders must be decked down 0.010" to compensate for the too-thick head gaskets that we get in the kits today: the OEM ones were made with asbestos, and this ended in the 1990s. The head gaskets all got thicker by about 0.8mm (0.008" or so) with the new materials, so any oil ports that pass thru the head gasket need correspondingly thicker O-rings to seal them. I got a 650 (1979) about 2 years ago that was an oil-soaked dribble in my garage to fix, and this was the problem with it.