I'm not sure on the '99 model but on the '03+ KXs the frames are the same except for the lower engine cradle tubes. The swingarm is different (I assume longer or something) as are some of the other bolt-ons.
I'm sure the frames you're asking about would have different part numbers but you could check part numbers on things like the radiators, swingarm bolt, air box, sub frame, and such to determine where the differences may be. In any case, there's no reason why you couldn't do the conversion with a 250.