I lined up my 66 fastback doors without any gasket/weatherstripping. It seemed to me that the door should match the quarter panel and lower rocker no matter what. When I later applied the weatherstrip, it was difficult to close the door at first, but after a few openings and closings and sitting shut for about a week, the rubber molded to the proper openings. If I had installed the new rubber first, I doubt it would have allowed proper allignment of the doors. The door catch and body latch post were also removed during this process. After alligning the door with the quarter and rocker, check the front of the door around the front roof pillar to see that it is reasonable, particularly if the vent window frame has been removed. I did mine with the door empty of any glass/mechanisms and the vent window frame removed. I later read that if this is the case, one should add an equivalent amount of temporary weight to the door to load the hinges during allignment. I didn't do this and had to make a slight further adjustment after adding all the inner mechanisms and glass. Overall, the gap between the quarter and door ended up about 1/8" + on average; and the gap between the door and rocker ended up about 3/16" to 1/4" on average. The front fenders were able to fit up to this door position pretty good with door to front fender gaps about the same as the door to quarter. This was a critical install for me as the doors and car body were finish painted before assembly so extra care was necessary. Good luck with yours.
