Mask, Mask, Mask. Decide if you are looking to build a concours car or a driver. Typically the crap inside the door is rusted and difficult to take apart. Window frames are SS and can polish up. If things go up and down well when lubed properly, I might consider masking and leaving well enough alone.
If a concours restoration is what you are after then by all means take it apart. But it is a total PITA to get it back together and readjusted once apart. It's all time, effort, and $.
If things look bad inside the door/ rusty in there then you probably don't have a choice. If it looks decent and you're only worrying about cosmetics, no one is going to see in there once the door panel is on.
IMO I'd rather get it done and drive it. Others on this list will offer different opinions I'm sure.