Have you ever trimmed auto front glass?? I've seen it done on U Tube. It takes quite a bit of care because of all the stress that's in the glass.
If it was me I'd put filler metal pieces on the sides and trim the top (or bottom) to fit without a rubber gasket. This way the windshield guy can apply his urethane around the opening and bond the glass directly to the body like all new cars. You won't be able to use your glass molding but it will look "CLEAN"....I know because I did my Barracuda that way. Also it will never leak!!
But you probably already have a plan, just thought I'd let you see what it looks like without the trim.
Treblig