I've done the notchback rear glass R&R a couple of times. Myself and other members here had the same issue... top of gasket doesn't want to lay properly to the headliner. Solution for me was to put the glass in the gasket from top down. Of course sitting the bottom of the glass in first was a heck of a lot easier than working against gravity but the finish was bad.
I had wondered why factory service manuals say to install glasses from top down. Now we know.
