jerrygolf,
When I had to have some replacement glass made from scratch, I created a pattern using 1/4" masonite rough cut to the opening / window trim to start with. Then with the rubber molding in place I continued to modify the pattern until a satifactory fit was obtained before I ordered the glass cut from the finished pattern. This seemed to work well.
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1934 Chevy 1 1/2 ton Farm Truck
1936 Chevy Master DeLuxe Series FA 5-window coupe
1961 Chevy Series 10 Fleetside
1963 Dodge M37