Did you check the inline filter at the carb inlet for blockages when the carbs were off?
https://faq.ninja250.org/wiki/How_do...fuel_filter%3F
Info about adjusting the idle mixture screws -
https://faq.ninja250.org/wiki/How_do...dle_mixture%3F
They shouldn't be far off, but there are factors that does make the adjustment change.
I would say you may have a fuel flow issue. How bad was the tank?