I had this issue with my 64 Fury convertible. They guy I bought it from brought a whole two door hardtop parts car just for the door. The top of the vent widow on the hardtop had a fin on it to close against the door frame rubber, while the convertible was flat to close against the top header.
I found the vent windows on eBay from a guy back east who was junking out a rusty convertible. I won the auction, but the chrome was so pitted I couldn’t use them. But I now had a pattern on how it was supposed to be. The hardtop and the convertible vents were the same, except for that fin. I had a friend who had a mill, and he clamped it up and milled off the fin. Looks good, and no one had noticed.