OK... Step one
Body/Neck refinish (refret?). The first step is to see if I can get off the new paint to get back to the original paint. I do this for both the body and the neck (on the neck, get down to the original finish). If this fails or can't be done, plan something else.
What about fretting at this stage? The frets feel REALLY low (but no real grooves). Do I worry about the frets before or after the body/neck work?