I also noticed the lack of a slow jet on all of the carbs. Should be down to the left of the main correct?
Yes. Looks like sabotage!
So #3 needs a rebuild kit. It feels like I can get away with just cleaning the rest due to the visible condition. I'll prob need to order the slow jets individually (40s I think). I saw another post where someone was running this setup and it seemed to work for him.
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The Cb550 should have #38 pilot jets.
I recommend you spring for genuine Keihin jets. Not all #38 jets have the same suction tube length or number and size of the emulsion tube holes, which make a difference.