If the clip is in the correct position, and the needle is stock unaltered, I'd then measure the Jet opening for the needle.
In short, if the carbs are set up in stock config, I'd look for reasons why your carbs don't behave like every other set of 550K carbs in the world.
In other words, if I found one of the forks bent, I would not simply bend the other one to match.
If your example carbs in perceived original setup configuration do not operate the same as the majority population of like examples, then something is wrong with them to cause unexpected behavior. I would try and find out what about them is different than when they left the factory, as it is unlikely that when new the bike sooted up spark plugs regularly. What is different about your bike that requires a change to the stock config?
The alternative, as I see it, is to keep tweaking randomly until it is acceptable, or you get tired of fiddling with it.
Understand that mine is an engineer's approach. I need to know why it works or not. And, I'm not happy tweaking things I don't understand until it appears to work. Mechanics just replace and tweak until the complaints stop for that example, and don't care about why.
I don't have enough information about your carb set to make an informed decision. I don't have test data about wide open throttle mixture, I don't have information about throttle response from off idle. Only a general complaint about fouling plugs and poor mileage, for which I speculate an issue with the throttle valve. But, I can only speculate, the machine's tech has to find the aberration. Once that is found and firm decision can be made about correction or change direction.
At this point, if you cannot find a reason why your carbs don't behave as predicted, and you want the most expedient way of getting the bike operating as you like, then get a different carb set.
I should have asked this earlier, I suppose. But, was the float height checked, and the fuel levels in the bowls verified? If the fuel levels were too high excess droplets would make the operation too rich and yield similar symptoms as you describe. Were the float valves replaced with aftermarket? Reading some of Hondaman's recent posts about the spring pin strength, altering those springs would require a change to the stock float height measurement. It makes perfect sense, to me.
Cheers,