The biggest hurdle to get over on a Willys is the doors, the stock doors drop badly because the hinges are so close together, its all about leverage, your hinges are very close together compared to the width of the doors which is not good, everyday physics tells you its not right. Do you have bearjaw locks ???
I would imagine the door is moving in the aperture, some decent weather stripping will help no end I would think but in my opinion a upper hinge is needed or the existing hinges further apart.

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