I took a look at your pics and did not see anything extraordinary and nothing to cause undue alarm.
1) Not a big deal whether the car is sanded before gap adjustment or after. The important thing is to make adjustments up to factory specifications where needed.
2) These cars were painted at St. Louis with the doors mounted. Doors do not have to be removed for a repaint. Some folks remove them, others leave them in place. I painted both of my cars with the doors in place.
3) Door glasses can be removed for a repaint, but do not have to be removed. The door glasses had not been installed when the car was painted at the factory. I've done it both ways. I painted my '68 with the door glasses removed. I painted my '80 with the door glasses in place.
4) I agree with you. If you have new door hardware, I would remove the old, repaint, then install the new.
5) Rear glass may not need to be removed. The excess silicon might be removed/cleaned up with the window in place.
6) Trim and weatherstipping should be removed prior to sanding and paint with the exception of the windshield and rear glass. I would leave those in place and the existing weatherstripping intact. Moot point if you have new weatherstripping for the windshield and back glass.
7) Doing paint prep with the car outside is not a problem. You want to ensure the car is not painted in the open air.
Some folks remove the headlight assemblies prior to paint and paint them separately. It was done both ways at the factory: early cars had headlight assemblies painted separately, then installed. Later cars had the assemblies in place at the time of paint.
:thumbsup: