So I haven't updated this in a while and just wanted ya'll to know it isn't a dead project.
I took the 450R engine out and built a CRF450R with Aprilia RXV front and rear suspension.
I got a good deal on a disassembled '06 CRF450X engine and it is currently mocked up in the CB350F frame. I had issues with the 450R kicker hitting things and the electric start will make my life much easier.
And for anyone that's curious, the only difference between early ('02-'04) 450R engine mounting and 450X engine mounting is the width of the mounts. Some careful planning and a few spacers will allow you to use any (at least up to '08) CRF450 engine.