You can't run 530 oring chains on the 550 without modifications. The wider chain will chew into the engine cases. If not when new, then it will after the chain and front sprocket wear some.
Cold run issues could easily be choke related problems. You are using choke, right?
I would check that the choke butterflies were closing fully when actuated. And, that the fast idle adjustment is holding the throttle open enough during warm up.
Choke can be time consuming to adjust at the shop. Because, the engine has to be cold to fine tune those idle speed adjustments.
Think about it. Rebuild carbs, get it running and adjust the carbs to run while warmed up. Can't adjust choke now. Gotta wait till tomorrow morning. Then next day, start bike, make some adjustments and, well now the bike is warm again. Did you make enough adjustment? Gotta wait till tomorrow morning again to find out.
Anyway, it could be that the choke cable slipped from vibration and you can't apply full choke. Simple to check, actually.
Another thing could be the spark plugs. If the shop thought an oring chain would work like it does on a 750, they might have put in 750 plugs, too. This will make the 550 into a cold blooded beast. Won't want to start and has to be totally warmed up to be ridable. 550 plugs are a hotter heat range than the 750's plugs. You should have D7EA plugs in the Cb550 (NGK brand). And, there should be no R in the spark plug number! Your spark plug caps have all the resistance needed for the ignition. And, putting more resistance in the spark plugs themselves will just make spark weaker for starting.
Finally, I'd like to know where you got new rubber couplers between the air plenum and carbs. These have been un-obtainium for years now. There's a LOT of us that would like to get new ones.
Cheers,