I had the same issue. Without any weatherstripping there was no gap but the door was sitting too far in. I tested with a slimmer wheaterstripping type, yep, that did the trick. However, at highway speeds I got the "whistle symphony" from air leaks. So, now I have two types, a thicker type following the front/ upper portion of the window, and a slimmer version for the rest. It´s not perfect, but much better.
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