This is a four-cylinder isn't it? Do you have the correct vacuum guage for the four? If you don't i recommend you take the bike to someone nearby who does and have the carburettors tuned and synchronised. Also it might help to pull the carbies off and give them a thorough clean.
Effectively, my advice at this stage is to give the bike a good service; carbs, ignition timing, valve timing, tappet clearances, cam chain tensioner, oil; the works. Even if these actions dont stop the bike from running poorly at this stage, it's something that will sparkle the engine up a bit when it is back to normal.
as i say i dont know much about 550 hondas, but if you're getting a good spark at the right time, the only real possibility must be the carbs - slack cam chains can affect things badly, but not usually in this manner.
heres hoping you find the issue,
Blue