Don't want to discourage you...but I think that swap would be a tremendous pain in the butt. The CL100 has a single downtube frame that ends at the engine, the CR's use a cradle frame...the geometery of the engine space in the frames are totally different.
Only feasible way I could see to do it short of having a machine shop is to get a CR frame and cut out the section of frame that mounts the engine and graft it into the CL frame.
Might be easier to convert a CR125 into a Cafe.
The upside is....if you are going where I think you are going...is one bad ass little 2 stroke 125cc Cafe bike that you could sneak past the authorities using the CL frame numbers for registration and such. With the proper work you could have a 120mph CL100
If I had a ton of spare time and a lot of tools (I do have the tools)...yeah I guess maybe I would give that a try. You'd want to update numerous suspension components on that CL frame to handle the HP and speed of the CR engine.