I resolved the mirror adjuster issue, at least temporarily, by wrapping it up in foam and securing it out of the way.
The door frame issue was resolved with a little cleaning, welding (I'm new to welding and desperately need the practice so I chose not to just use a bigger washer) and grinding.
So there, that's a couple minor issues I don't have to deal with later. I need to get new weatherstrip for the door before I try to re-install the panel. The original ones are crumbling so no point in trying to fit the panel with rubber that won't be used in final assembly.