You can't really seal the door window opening. The 'fuzzy' seal there is primarily for anti-rattle. The lip-type seal that newer cars are using does a much better job, but still can't keep all the water out. Instead, take your door panels off, clean out the bottoms of the doors and make sure the door drains are open. Then make your own weather seals from a sheet of heavy mil clear plastic film. Include flaps that are a little larger than any openings and make sure the bottoms of these flaps hang inside the door. Seal it all up using strip caulk or weather strip cement. You can even test it for leaks before you install the door panel. If you need something to look at for reference, check out some cars in a wrecking yard.