The gap between the window and the vertical weatherstrip can be remedied somewhat by adjusting the quarter window. There is an L shaped bracket that the entire quarter window assembly sits on, and this bracket bolts to the rocker. Loosen the bolts that bolt it to the rocker and and pull it towards you (towards the inside of the car). This will cause the quarter window to kick out and the seal will come closer to the door.
For what it's worth, my door is original, my window is original, my quarter window is original, and my quarter window vertical weatherstrip is Ford tooling and it still doesn't make a super tight seal there, even with maximum adjustment.
69 Mach 1 428 SCJ with drag pack