There could be a few things going on.
Have you tried to set the idle speed when warm?
Do the idle mixture screws have any effect?
Did you check the float levels?
Did you sync the carbs?
Is the gas fresh?
It does sound like the Pilot Jets could be partially plugged. Carb cleaner alone may not completely remove all of the deposits. You may need to use (soft) fine wire to gently clean the inside of the jets. Just being able to see light through them doesn't always mean they are completely clear.
Also try removing the (oiled) air filter and see if it changes anything. It's really easy to over-oil the filter, and it will affect how it runs from idle to WOT.
Use this section for reference -
https://faq.ninja250.org/wiki/How_do...n_the_carbs%3F