Did you remove the caps from the idle mixture screws, clean the passages, check the o-rings, and set the screws to 2.5 turns out?
Once that's done and the engine is warm, set the idle speed to 1300 and sync the carbs.
If it won't run well after that, it could need additional carb work or other work like valve adjustment.
Valve adjustment info -
https://faq.ninja250.org/wiki/How_do..._the_valves%3F