When the window is up there is a bit of a gap between the top at the back end of it while the front is in the channel. That's what makes me wonder if there was a change in door glass when they changed the roof? I don't think it's the way the window is installed because the front and back edges look like they fit inside their channels properly and the vent window fits properly and it's parts are identical on both doors. I'll try to get a picture.

My main reason for wanting new glass is more because the old stuff is scraped up and pitted. I have new door seal kits but don't want to put them in with the old glass.