Door Adjustment Question, Another question about doors n' stuff Options

[BeatNavy]

I did a bunch of searching and couldn't find an answer to my specific question, so I am turning to the brain trust...

I spent two weekends this month refurbishing my doors. Goal was to treat rust, rust-proof, and reseal. Before removing the doors I scribed a marker around the outline of the hinges to try to get back to where it was mounted before. Good idea, and yay for me.

However, after all was done and I remounted the doors, the driver's side door in particular now has a noticeably smaller gap at the back. Perhaps I didn't get the door mounted as exactly before even though it's close to the mark I made. I DID find from searching that what I probably want to do is raise the door slightly, which would probably even out the door gap AND also help with the seal to the targa. All good.

But when I loosened up the hinge bolts the door would not move any higher despite a fair amount of finagling. Either I need to finagle more (and with a stronger helper other than my wife) or something is preventing additional vertical movement. I'm pretty sure the hinge plates are moving freely inside the door. So here's my (likely stupid) question: does the door stay need to be loosened as well for this process? If this is correct, is this done with those two bolts on the outside of the door? If this is not correct, back to finagling....