How did the carb diaphragms look? They can get damaged easily and give you all sorts of problems.
That, and the carbs may need more than just spray cleaner...
The Needle Jets ("collar") are in place correctly - right?
https://faq.ninja250.org/wiki/File:Jim_carb_2.jpg
Idle Mixture screws have a spring, washer, and o-ring on them?