Is the gap between the rubber seal and the front glass? And is the door glass tipped outward relative to the rubber seal?

If the rubber seal doesn't meet the door glass, the adjustment is likly needed at the rear window track.

Both the door glass and rear window can be adjusted slightly from within the door or body space. You would need to remove the interior panels to get to the adjustments. Rear windows not rolling up and down are likely the result of the rollers either worn, gunked up, or broken. New rollers are relatively cheap, but they are a PITA to get in. But they make the windows go up and down like new.