[Macgyver]

I'm getting ready to paint a Mustang and hope I can get some help with disassembling the car. I'm not sure of the year, I can't find out until tomorrow morning, but I believe it's a 95-97 model.

I need to take the drivers side door off to weld a patch panel at the bottom. I've never taken a door off a vehicle. If I remove the bolts on the door side of the hinges, will I have problems with alignment when I put it back on?
or
What is the best way to remove it?
It will be a color change so I would like to take both doors off to get a better finish in the jambs.

I need to remove the panel/strip between the door glass and the roof/windshield. I see there is a bolt at the front but how is the rest of it held on?

Thanks.

[Macgyver]

Here is what I need to remove. The pieces highlighted with blue. On the piece above the door, I removed a bolt at the front then a couple push in clips along the windshield. It gets very difficult at the roof line. Are they bolted from the inside? I didn't want to pull any harder to break anything.
Also, I'm guessing the scoop can be removed from the inside. Correct?

I've welded a couple patches in but waiting for the clearcoat to arrive before I strip too much of it.