Brian, Your doing a great job on your car and everything is looking good.
I had the same problem trying to hook up my adjustable mirror. The new upper door panel was too thick and the threaded adjuster was too short. I carefully pulled up the vinyl around the hole and removed the extra fill that was extruded under the vinyl then I carefully hammered the metal in so that it would be closer to the door frame when installed. I struggled for a while until I could get the threads to catch and pull everything together.
Whatever you do I know that you will make it work and look good, you always do.
(Picture before operation.)
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