I have read many times to use 87 octane fuel. Perhaps the 89 is part of the issue?
https://faq.ninja250.org/wiki/What_k...hould_I_use%3F
Are you running out of fuel? Do you have it on reserve? Have you serviced the pet cock?
https://faq.ninja250.org/wiki/Rebuil...tcock/fuel_tap
Have you been able to set the idle adjustment to around 1,500 RPMs?
What about the built in fuel filter ( if it has one )? It is recommended to remove it, and replace it with an aftermarket one.
https://faq.ninja250.org/wiki/How_do...fuel_filter%3F