You need to start thinking in terms of throttle position when tuning a carb.
Basiclly, idle mixture is controlled by the Pilot Jet with additional fuel being metered by the Idle Mixture Screws.
From there (1/8 ) you transition mostly to the Jet Needle (and Needle Jet - which is not adjustable on the Ninja ) setting through around 1/2 throttle and above where the fuel is eventually controlled almost totally by the Main Jet at WOT (Wide Open Throttle).
If you cruise at 1/2 throttle and it doesn't fuel properly, I would look mostly at the Needle Jet - but the Main Jet also is a factor. It's recommended to set the Main Jet first (WOT running). When you get it to run properly at WOT, focus next on the Needle setting to get smooth running in the 1/2 throttle area. After that, tune the idle mixture screws to get a good idle. If you are 3 turns out or more it indicates the need for a richer Pilot Jet.
Your Idle Mixture passages may be partially blocked if the screws have little or no effect.
I would also confirm that you don't have any vacuum leaks, and look at the plugs.
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