Window door glass adjustments

Does anyone know exactly in which order I should be adjusting the vent window frame, door seals and then quarter seals on my 65??
I am putting all new rubber and catwhiskers, but I think i have the vent window frame set wrong, causing the door not to be able to shut with the window up. This picture shows how much gap there is between the vent frame and the roofrail retaining molding.

Any help would be appreciated!!

vent window1.jpg

vent window 2.jpg