I still don't think you'll be able to reproduce the exact positioning using the Kyosho mounts on the OFNA car. They will still be off, I'm 90% sure of it. For example, I could put the Mugen body mounts on an Xray and vice versa, but it still won't change the relative position of the shock towers/body mounts in relation to the wheelbase unfortunately.

As for lining up body holes, crush up some chalk (chalk for blackboards, any color which works) into dust, and put it liberally on top of the body posts. Lower the body very carefully on to the body posts in the correct position, then drill through the chalk marks on the underside.