Here's a tip on painting it together without the paint laying over or essentially bonding the panels together like you're worried about. I learned this from a top notch Mopar restoration shop. Let's start with your fenders/inner fenders. Get some longer fasteners. Let's say they are 5/16" like in the case of my 40 Ford. Get some 7/16 or 1/2" nuts. Mask off the inner fender area you don't want body color on. Have a helper help you hang a fender and use nuts to space the fender away from the body and then bolt it on in as many holes as it takes for the fender to be firm and not floppy during prep or sanding.

The doors I remove the latch and tape off or remove the striker. Just be really careful when opening/shutting the door to not push it in to the jamb if that is possible. I've seen guys make a short stopper to go in the striker hole that would contact the striker plate or striker to hold the door firm but out a little to not contact the jamb etc. You'll need to or want to open and shut the door to get the lower hinge covered and access the jambs.

I'm currently in the boat of I need to paint my front clip and fenders after I shot the body. Luckily for me I screwed up the rear quarters so I will be re shooting them so hopefully my metallic lay out is the same. I have very little space like you said so it takes planning and a lot of cleaning. Fall is a great time to paint with less humidity usually, and less bugs. I hung fly strips up all over and I actually started late in the evening because the kids were inside and not coming in and out all the time. I'm no pro painter but I like learning and I need to learn as I have a lot of projects and they all need painted. I can see so many flaws in mine that I want to re shoot the entire thing. Everyone tells me to just get it together and worry about that later. I've been passing fliers out at a lot of shows lately and I notice several of the top winners at these shows have several blemishes or things I feel awful so I figure my friends are probably right and I just need to get it together and off the wooden stands. PS, mine is another 10yr + build on here so don't feel bad. Haha