Carbs...carbs...carbs...
Something isn't right. Did you remove the idle mixture screws and clean the passages? O-rings on the screws look good? Set to 2.5 turns out for starters? Carbs bench synced they checked with gauges?
Did you check all the small holes in jet and jet holder? Is the Needle Jet (collar) in place?
https://faq.ninja250.org/images/e/eb/Jim_carb_2.jpg
Rubber diaphragms in good shape? Slides rising and falling correctly?
Ducatiman doesn't like Starter Fluid (Ether) as it's bad for the plastic and rubber parts.
There should be a fuel filter inside the fuel line at the carb inlet that should be checked and replaced if needed.
Check that the petcock is flowing properly and the vacuum line to it is in good shape and attached firmly.
Read through this section for more ideas -
https://faq.ninja250.org/wiki/Cleaning_the_carbs_1