The square foam blocks are slit partway through in the lengthwise direction and placed on the top/inner edge of the inner lens. That way when the outer lens is installed, the inner lens is held in place under tension.
The glass windshield can't leak, only the rubber seal or bad sheet metal. As Dr Fate mentioned, you should more thoroughly investigate where the water is coming from, then proceed.
These are usually three-piece stainless. #1- up the "A" pillar to the windshield/roof corner, #2- a corner piece, #3- long strip to the back. When installing there is a foam strip between these retainers and the body.
Each year was different. 1967 has the large "383" behind the front wheel, 1968 has "383-s" in the hood insert and 1969 has the small "383" ahead of the front wheel. In 1969, if you ordered the stripe the "383" was there.
Door fit is important but more likely your latch is gummed up with dirt. You should be able to shoot in some spray lube with the glass down. If not, remove the door panel for a clear shot.
The way the hinges are made causes a lot of "slop" when in the open position. There is no "adjustment" for this other than tweaking the hinges themselves or their pivot pins. Usually we are content with proper alignment when closed.