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Screws very similar to your rusty flat head screws retain the stainless trim at the tops of the doors on my '57 Shev-a-lay 2dr hdtp. If your car has any similar trim, that might be their purpose on it.
The sill plate screws, 9414799, are #10-16 1" with a # 8 head in chrome. Your screws are too small for that application.
The little short ones look like the side head light screws on the outside trim, however would only need four.
Those 4 screws are 9420684, #8-18 1/2" type BA, check your AIM and see if used elsewhere on your door as suggested.
Those tiny little rusty ones are identical to the screws that hold the outer window seals on my convertible doors. It is the rubber strip that runs along the top of the door and those screws are not visible once the door panel is on. I believe they are called Door Glass Outer Window Moulding Screws.
Yes, Wyndham is correct regarding the six rusty screws with the flat tops. We just took a set of doors almost completely apart on a 66 last week and ended up with those same screws. Top Flight calls them "C2 1963-1967 Chevrolet Corvette Outer Window Seal Screw Set. - CA"