The fact that bike is not running correctly means carbs are not fully cleaned. Sure, they may be better than before, but they are not factory-fresh as when they left factory.
Unfortunately, due to regulations, "carb cleaner" liquids are nothing more than weak carrier solvents without real cleaning/cutting chemicals. Back in old days, carbon-tetrachloride was awesome. I'd spray it on inside of my sprocket-guards and gunk would just slide off like hot butter. Then it was banned. Next best stuff, trichloroethane worked OK and was around for a while. But it too was banned.
When I spray stuff available now OTC onto my sprocket-guards, it runs off almost clear, having dissolved no grease and oil at all (I'd probably get better results peeing through carbs). So I don't give it much hope in cleaning carbs which have gas that have dried into plastic varnish. This is poly-vinyl cross-linked material similar to tung or linseed oil used in the old days as clear-coat/varnish. It's never dissolving again.
What is needed is mechanical scraping/flossing of all fuel-circuits in the carb-body itself. The jets are easily done with copper-wire or guitar string. You'll also need to soak carb & dis-assembled jets in ultrasonic cleaner for couple days. Then pressure soda-blast through all holes and passageways. One final step I do is drip dye I make with food-colouring through the passages to make sure it comes out other side. Same with every single hole in jets, especially pilot-jets with their multiple tiny holes. Each and every hole should have dye coming out before I consider them cleaned.
Some related threads:
https://www.ninjette.org/forums/showthread.php?t=322846
https://www.ninjette.org/forums/showthread.php?t=321223
https://www.ninjette.org/forums/showthread.php?t=315193
https://www.ninjette.org/forums/showthread.php?t=317977
Some of really good mechanical guys on here, guys who can rebuild engines using only their teeth with both hands tied behind their backs, have had to disassemble and "clean" their carbs more and more thoroughly 3, 4, 5 times before it was as clean as factory-fresh condition.