Definitely do a FULL tune-up.
New points and condensers, new plugs and caps (and trim down the wires 1/4 inch or so to get fresh copper, adjust valves, adjust cam chain, CLEAN CARBS, then RECLEAN CARBS, and finally CLEAN CARBS AGAIN.
I cleaned the carbs 3 times before I got them perfect. pull all the jets out, run some copper wire through them to ensure nothing is clogging them. Set the floats (12mm I believe on the 550) ensure the float needles work properly. Buy a couple cans of carb cleaner and go to town on them!
you don't need a carb soak unless they're REALLY bad.
After all that's done, you're ready to sync the carbs.
If you have access to a compression tester, go ahead and check the compression...either way you will have to adjust the valves.
If the bike has under 50K i wouldn't worry too much about the internals, these motors run forever!
If you don't know how to do any of the above tune-up procedures, search...there is a lot out there. Download the manual and read.
Mine was in a similar situation when I got it. It was able to get it running on two cylinders, and it sounded like there was loose metal in the engine. After adjusting the cam chain and doing ALL the procedures, it runs like new.
Good luck