I have fitted a honda xl 500 motor into a klx frame, there are issues...there is very little space for the carb (requiring a long droopy intake manifold), due to the frame back bone dropping down to the seat area. May be different with a 250. The bike was ...ok ( a lot of work), but given the choice id go husky, and ive ridden a white frame husky /xt 500 hybrid as well, a better option imo.
I have also fitted a xr200 motor into a klx, along with a modified xr 200 air box, all fitted easy, tightish at the top, miles of room down at the lower cradle/ towards the front of the motor.