You don't need the bigger Pilot Jets with a stock airbox and pipe. We ran ours with pods and a leaky exhaust with the stock 38s.
We ran 108 Mains. 105s may be too much for you.
I would say you need to adjust the idle mixture with the Idle Mixture screws. With 42 Pilots you won't be very far out -
https://faq.ninja250.org/wiki/How_do...dle_mixture%3F
You will always get a hesitation when cracking the throttle hard with CV carbs.
Shimming the needles will richen the midrange slightly -
https://faq.ninja250.org/wiki/Washers_for_carb_needles
I'd also sync the carbs if you haven't.
This section may have some helpful info -
https://faq.ninja250.org/wiki/Intake