The door panels do sit out a little farther than the rear panels. They should butt up against the outside edge of the windlace, think that's what it's called. It's the trim strip that runs down the edge of the door jamb. If the outside of the door is pretty flush with the rear quarter there's not much else you can do. Maybe a picture of what you're talking about would help.
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Hank
70 Chevelle SS396(454), M20, 3.73
My Chevelle
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