Damian, if you've ended up with no joint line or a badly defined one, I would be tempted to fill it over rather than try to simulate one. Although if you did, lead-loading might be advisable for longest lasting looks.
That joint line is pain to get right at the best of times, as any slight misalignments, manufacturing errors or tool marks from the alignment process all get magnified as soon as paint is put one.
On one side of my car, in spite of great care taken, there are a couple of places on the very sharp radius of the flange on the wing where the paint has chipped away. I think that the sealant in the gaps doesn't help with this. I'm currently scratching away trying to do as invisible a repair as possible.
I can't help you with the hinge pin. As far as I'm aware, don't these have nylon bushes? Where is the pin stuck? Do you have a photo? You can get hinge-pin removal tool but I've not used one. On my camper, which has very basic hinges, getting the pins out is the only realistic way to remove the door. It looked impossible; but I burned off the paint, wire brushed it soaked in penetrating oil repeatedly over several days, and then used a tapered punch and 4 pound hammer to get them moving. All six pins came out textbook fashion. I treated myself to an early tea-break that afternoon.
As you say...you
"will get them out somehow."
Good luck.