How about posting a couple pictures.

the Willys only has about 1/2 inch lip all around the door and it was never a good fit. Most of us just put some "rubber dots" in the body for the door to ride against ans then use "windlace" piping for the seal on the inside.

Windlace is P shaped molding/seal material that is either nailed if wood is available or contact cemented in. It fell out of favor in the 60 I think.

I nearly cut the door in half sectioning a piece out of it to make it fit. I also cut the posts off and re-glassed them back together so the top of the door fit properly. I just saw a nice steel car and his doors fit much worse than mine did before I fixed them.

Even my hood fits better than his.