Re: Painting sequence
My suggestion is to paint the whole car at once. I would leave all of the glass out and make sure you paint the areas where the window felts go etc. You won't get as good of a job when masking. As far as the front and rear window channels go, they should be stripped to bare metal and sprayed with epoxy primer. You don't want paint on them when the urethane goes down to seal the glass. Painting them means the urethane will only be sticking to the paint and if it doesn't bite into the epoxy well enough then the thin layer of paint is the only thing holding your windows in the car.
There's nothing wrong with being stupid as long as you know you're stupid, it's when you're stupid and don't know it that you become dangerous.