I should be getting the engine and head back within the next two weeks. I am not sure how much more mocking up I need to do at this point to feel comfortable with cutting, prepping and painting the frame. I am going with paint because it feels like there is 100% chance I will scratch the finish on the frame and want the ability to touch it up.
My next steps as far as I can tell:
1) Pull everything apart.
2) Cut (tabs, center kickstand, etc), sand the frame
3) Fit the seathoop and seat.
4) Cut and drill an aluminum pan for under the hook for electronics
5) Get someone to weld the seat hoop on
6) Prep the frame and swingarm for paint.
7) Paint the frame and the swingarm.
Decide if I want to paint the head and valve cover.
9) Assemble the engine.
10) Get the engine into the frame.