Tomboy - paint or powder coat your engine before installing in frame, even better while disassembled (if you have it torn down). Minor scratches may happen, but use blue painters tape to protect frame and cases while installing, use some care, and you'll be fine.
Be certain to lay the engine on its right side and lower the frame onto it for best results to install/de-install.
A word about ceramic coats and air-cooled engines: it's not really a good idea to paint the cases with ceramic paints or powder coats. Ceramic is a thermal barrier and will actually raise internal temps of the engine, not lower them. There are dissipative coatings (your powder coater may be able to direct you) that are better suited to the heads, cases and covers that should be used. Regular powder cost is even fine (or rattle can paint). Ceramics are best used on exhausts inside and out to protect the tubing and rider from hot surfaces.
Hope that helps-