The ONE thing I NEVER hear people say they've tried is cleaning the carbs.
Pull the carbs, remove the pilot mixture screw plug (air/fuel mixture screws plugs) so you can remove the mixture screws for cleaning, and disassemble the rest of the carb.
Get some CHEAP Wal-Mart brand carb cleaner spray and go to town on all the passages.
Eye up the butterflies, using the mixture holes in the throttle bores as a reference point.
Install the flat valves in different locations. (do NOT remove the valve seats at this time unless you are replacing the seals)
set mixture screws to 3.0 turns out, and do not use shims at this time.
Do not install airbox at this time. Assemble everything else. And test ride.
If running well, good. Tune as desired from here.
If same, or similar condition remains. Remove gas tank after motor gets to operating temp, and look down the throttle bores to see if any one of the carbs is leaking gas up through the metering rod port (emulsion tube) (it should not be pushing gas up). THIS IS A COMMON PROBLEM WITH SOME OF THE OLDER MIKUNI BIKES. Means that the float valve is bad.
Could also be dirty carbs, a loose metering rod (cap is not on completely), extremely dirty air cleaner (doubtful), clogged fuel filter, bad fuel pump, etc.
My guess is the carbs are dirty and maybe need a float valve or two.
It doesn't have to be the right tool; Just one that works.