I have an RD350. I have a feeling that engine would feel massively heavy in a KDX frame, also too wide. No doubt it would rip, though. The RD's would probably be a little peaky for offroad work. They come with a 6 speed, and you need all six to stay on the pipe if it's at all modified. Stock they're a little tamer. You'd have to rig up an oil injection tank, or go to premix. The pipes on an RD and low slung and would be totally hopeless offroad. Any available expansion chambers would make it even worse.
Seems like a gigantic waste of time, honestly.
You can spend as much as you want on a CDI for an RD--There are a couple that I'm aware of, though I can't remember what they're called. Check out USA Two Strokers. One is made is from India, one is from Germany (MZ I think). Both expensive ($600+). Both are programmable, though.