I'm just not a fan of the aftermarket inline fuel filters on the Ninja.
If you look at the fuel line above your filter, you will see it's starting to buckle - which may restrict flow.
My suggestion would be to make sure the tank is clean, check the petcock filters to make sure they are clean and in good condition, install the OEM mesh filter inside the carb inlet, and replace the fuel line.
If it's still running poorly, the carbs need to come off and be properly cleaned, rebuilt, and adjusted.
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