I haven't a clue what I'm doing since this is really the first time I've done something like this so hopefully I'm going about it correctly.
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If I may make a suggestion on this point...before you go too much further, try to really be honest with yourself on what you want to accomplish in the end. Different goals require different approaches.
If you're looking to do a full restoration and make it look good as the day it rolled off the line, you really need to disassemble everything (taking hundreds of reference photos and individually bagging and marking all hardware as you go. If on the other hand, you are just trying to have a respectable cruise night special, you don't really need to go that far. If repaint is part of your near future but you aren't looking for car show perfection, you should still consider that a decent paint job requires the removal of everything touching the paint.
I bring up this last part because once you start fixing leaks around front and rear windows, you will discover that doing it right means removing glass, dash, anything in the area that a welder can burn. Then you will probably want to replace trim clips which typically are rusted in place. By the time you clean, weld, and grind, you then will want to paint that whole area for protection. You see where this is going.
I dove into what you're doing on my first Mopar and one thing led to another. I owned the car for only months before I started "fixing a simple leak" and many years later along with tens of thousands of dollars, it still wasn't done. Came out beautiful in the end but it definitely was not what I planned in the beginning. Primarily because I really didn't plan.
You seem to be figuring it out and I don't wish to dampen your spirit. In fact, the opposite. Many folks get in too deep too soon and get discouraged. In my opinion, there is value in really planning out your project. I plan and over analyze too much on my projects but it's paid off for me in the end.
Keep in mind that there will always be surface rust here and there on even the cleanest cars. There is lots of overlapping sheets on metal everywhere and while the factory used sealers, water gets into all these joints. Even if you manage to get it all, it will reappear here and there. Especially if you drive it.
I like your car by the way and the pictures look good. Doesn't look bad at all. I'm anxious to watch your progress.