Take solace in knowning that you're amongst millions and millions of new Ninja 250 owners who've gone through this. I went through this exact problem when I got my 1st 250 years ago.
Bottom-line? Carbs aren't factory-fresh clean! Bike ran perfectly fine when it left showroom floor and will again when they get cleaned to factory-fresh clean. Many, many expert mechanics have had to pull their carbs 4-5x for ever deeper cleaning before they got them factory-fresh clean. One guy had to pull his carbs 10x !!!
Note, "carb cleaner" sprays no longer work due to removal of chlorinated compounds. Don't even bother with using them... Maybe just flush chads and remnants from real cleaning... which is.... scrubbing!
1. disassemble down to every last nut, bolt and individual component. If you can take it apart further, keep on going until it's completely separated.
2. Poke out all bleed holes in jets, pilot-screw, emulsion tube, and carb-venturi with soft copper wire.
3. scrub out all hidden secret passages in carb-body with brushes and PEA-based fuel-system cleaner. Spray carb "cleaners" no longer work due to removal of chlorinated compounds. Might as well use pee since at least it has some ammonia.
https://n4mwd.blogspot.com/2013/10/s...-passages.html
4. ultrasonic soak everything overnight
5. micro soda-blast everything to clear out chads and scruff from above steps
6. replace all rubbers: pilot-screw O-ring, fuel-rail O-ring, float-valves, float-bowl seals
7. set float-level and wet-test
8. sync carbs
On some carbs, even all this isn't good enough. I send to Gordon @
https://customcarbservices.com (ducatiman) and they come back running like brand new!