To remove the door top, I will reference that lovely picture above.
If you have weatherstripping, you will have to unfortunately cut it right at the top of the lower door section, front and rear, a good sharp knife will make the best, smallest slit.
First remove the large silver cover plate, then roll the window down until you see the arm and sliding track from the window regulator. Reach in hole or use large soft faced clamp, like a Quick Grip or something and hold the glass from falling down the tracks. Remove 4 screws from window crank and slide out and forward until wheel comes out of slide on bottom of glass. Retain grip on glass somehow, again the clamp works good. If the glass falls down, there is a rubber faced stop at the bottom of the door, but it is a pain in the butt to slide back up, you need spidey hands to do it. The window stop is held in with the two bolts closely spaced at the bottom of the door below the large access cover, do not remove these. Remember position of crank to arm orientation if you want it go back in the same way and crank up and down to the same spots, relative to where the inner door crank handle stops.
Next remove the 4 bolts located roughly in line with the window tracks at each quadrant of the door. There are also 2 bolts on the front edge of the door. They can just be seen above, in front of the hub instruction sticker. Next turn the wing window to all the way open. There is a limiter piece inside the door, you can see it if you take out the grey round plug at the front of the door below the wingwindow. If left closed, this will catch and not allow removal. Also the two window tracks kind of catch as they come out, you will need to push them slightly away from the inner skin of the door. This gets the welded nut flanges over into the holes they are going to pull up and out of.
At this point things may be rusted up, particularly the front mount below the wing window. Some gentle tapping with a soft faced mallet and wiggling may break it loose, could take rust penetrant too. Once it is broke loose slide the whole thing up, holding on to the glass, a helper is very nice to have at this point. Remember the tracks are going to catch as they come out as noted above. Once everything is moving, the slide track at the bottom the glass may hang up against the rubber and felt wipers in the lower door top, you have to gently force it through. Once free, hold onto the window tracks, as they may spread and drop the glass out, the glass is thick and heavy. When pulling through the wipers, the retainers may be damaged or dislodged. They are held on by tiny wire clips with a round top and an "X" bent into them that just stick through the holes in the retainer/wiper/door top. If they fall down into the door a long magnet may find them again.
I store door tops with the glass slid out and safely stowed separate, or upside down behind a cabinet or something, they should be safe there. A piece of wire can be placed across the tracks so they don't spread. Wing window can stay in.
Cheap plastic clipboards make great raw material to make a patch for the window crank hole.
Technically the plastic and tar inside the access cover and the gasket under the window crank do keep out dust as the water weep holes in the bottom of the door are exposed to the outside beyond the weatherstripping. Dust could migrate out of the door from those openings, mainly just leaves a funny static dust stain around them.
(which wasn't easy because the door is f-ed up.
