the 500 carbs are fine on the 550, they were just jetted differently from the factory
If you dont have the airbox to put back on, your just going to have to work with what youve got, either way youll definiely need to drop the needle clip to the 3rd slot to richen up the mid range, if youve already got 110 and 115 main jets throw either of them in, 115 if your exhaust is particuarly open and see how it pulls with wide open throttle
I have seen aftermarket pilot jets that are alot shorter than the stock keihin jets, do your pilot jets have a logo on them? oem keihin is always better. That may be causing your idling issue.
These adjustments need to be made to run right with your set up anyway, regardless of the idle being the main concern right now.
what rpm are you idling the bike at?
Also what position is the choke lever in when your running it, it wouldnt be the first time the position of choke on and off was confused (the thump tab on the choke lever becoming horizontal is full choke)
Phil