First thing I noticed was that the plugs have different deposits on them. The far right is not running the same as the others. Not the current RPM problem. But, it will be an issue later on. The new plugs should all be sparking as required in their present condition.
Has there been a vacuum sync?
It sure does idle poorly.

While I've never seen a CB550 operate with that specific behavior, were it mine, I would check the fuel height in the carb bowls with the clear tube method to find exactly how high the fuel level is. A too high level could explain the the symptoms.
Did you say you had to readjust the floats a lot during the rebuild?
Another possible check, is drain each carb bowl in turn (After turning off the fuel valve) and measure the volume each holds. I don't know what it is, off hand. But, if you choose do do this, I will measure mine for comparison.
Not to insult, but I'd check some of the following if you brought it to my garage.
Have the main jets fallen out? They have a spring clip that holds them in when the bowl is installed. Still have all four spring clips?
Are the choke plates staying in proper position? They have a spring/ball detent which is supposed to hold them at set position.
Is there a rag in air box or air filter box?
The picture below shows the jet retainer spring and the float installed properly. Please verify that the float is right side up.
Be aware, it is frustrating for us too. We want to help, and are searching for clues that you must provide to solve the issues.
I'd venture to say that your bike has an issue none of us have seen exactly before. Whether it is mechanic induced or a part failure remains to be seen.
Have you tried different gas?