See the dark finish along the edge? That's what I mean. Looks like it was painted. I'll probably reuse that built up part again instead of trying to fab it, because they appear to have tapered the rubber sections in the stack.

Bryan - the leading edge of the quarter glass frame is usually painted a satin black. It makes for a nice finished look, your door gasket color will blend right in.

What's that rough residue along the forward edge in second photo?

It is glue from the original door seal. The the pinch weld from the bottom of the door frame rises and stops at bottom of the quarter window frame. The quarter window has a part that extends forward to continue the pinch weld to the roof.

Some people glue or affix additional foam sealing in this area.