Is that clip in your photo bent ?
I think they are supposed to be flat. I have a 68 Fischer Body Manual that I got when I got my 68 LeSabre convertible. It says all the windshield molding clips were held on by a rivet stud on the bottom molding and some kind of snap retainer for the side pillar & top molding. Seeing you have screw holes - yours might of been modified by a previous owner / body shop.
Where the molding attaches to the clip, that portion of the clip angles away from the window channel. When the clips are installed in the window channel The U shaped center piece is what the screw goes through.
The way you have your clip in the picture, the left side of the clip is what will attach to the top edge of the top molding. The bottom edge of the molding just sits across the glass.
Hope this helps. A glass shop might also be able to advise you.
Good Luck
Harryface =D8=BF=D8
1991 Pontiac Bonneville LE 301,650 miles