One thing that seems to make a difference on these 2nd gens is the brand of seals. Metros are too thick on the door seals. Precision are too narrow, but Fairchilds seems to be the best. Have you checked to see if there is a stack of shims in between the door hinge and cowl? It sounds like to me you either have some smashed/worn door seals or someone has shimmed the door out trying to get better alignment with the fender/quarter.

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