I like the look with no side moldings too, makes a huge titference. When you are trying to decide whether to fix or replace that door, keep in mind that what you have is already the right color, has the right lock cylinder in it, etc. I got lucky when I replaced the door on my old one, found one that was already black. I just put the whole thing on and skipped even changing the lock.
Something I have found to be helpful when checking my bondo-shaping progress is wetting it with wax and grease remover sprayed from a gun. This allows you to see it wet for a short time, long enough to study the reflections on the contours of the panel. Less time consuming than spray paint, just sayin. You might want to cover up that rocker molding until you're done with the mess, too.
Do you have a plan for the roof ditch moldings? Planning to paint those too? I would have a tough time even deciding whether to remove them or not.