1) It appears the glass is still out, correct? 2) The glass channels for the main window would not normally come up that high in the door frame if the glass was in and the window was all the way up. 3) You have not installed any weatherstripping on either the inside or outside of the window opening.
The empty window frames are coming up too high when you roll the all the way up and because it comes up too far - it is pushing the bottom glass channel too far outwards.
So, I think you need to install the glass and then adjust. Basically the window needs to ride in the lined channel at the back of the vent window and match the angle of that "track"
2012 Mustang Boss 302 #1918, Competition Orange. FGF replacement 2006 Mustang V6 Pony, Vista Blue. Factory ordered. 2019 BMW X3 (Titled to the wife, but I'm always driving it for her. So I'm claiming it) Old projects, gone but not forgotten: 1967 FB 400, original CA car. After 22 years of work, trashed by the guy who was supposed to paint it. I had to sell it. 1980 Turbo Trans Am 1970 Mustang fastback, 351C 4Bbl, auto 1988 Mustang GT, 5 speed 1983 F-150 4x4, built 302 1994 Chevy K2500 HD 4x4, 454 TBI