It sounds like the carbs were not correctly 'bench synced'? On the 77/78 550 I recommend using nothing (i.e., not a 1/8" drill bit), but to set the carbs all to close exactly the same with the idle screw backed off. The #2 carb on most of the PD4x series carbs does not have a slide-sync adjuster, so make sure it is closed, then adjust the other 3 to also be closed. Then they will be better synch'd by default.
The last carbs (PD46x series) are very 'touchy' about this issue.
Are the carbs the PD46A, or PD46B, or PD46C type? The "A" type uses 14.5mm float depth while the "B" and "C" use 12.5mm depth. If the carbs are, for example, "A" type and the floats are set to 12.5mm depth instead of 14.5, it will run a little too rich and will tend to 'hang' at high idle when warmed up.
Also, make sure of the idle-mix screw setting: it should be between 1.25 and 1.75 turns, tending toward 1.5. Hopefully you have the OEM Keihin brass inside the carbs: with aftermarket brass (like from 4into1.com and other non-Honda sellers) will not mix correctly and will cause you to have to figure out your own jetting because theirs is calibrated differently: the size numbers do not match up with Keihin's numbers.