Haven't seen one for the Ninja 250. Here's a link to Wiseco big bore kits, which they make for a whole pile of different Kawasaki streetbikes (and other makes), but no kit for the 250:
http://www.procycle-online.com/bigbore/bbstreet_kaw.htm
When people go about improving the ninja 250's engine performance, for street use at least, typical mods include intake improvements/exhaust improvements/timing, rather than wholesale component replacement. There's no technical reason why more couldn't be done, but at some point the costs would be hard to justify instead of choosing a different bike to start with more power.