I am in the process of getting my car ready for paint and here is what I have done and up against.
I started out having my car media blasted. Originally, I wanted to do like you and get all the new metal welded in before I epoxy primed the car. I soon realized that was a bad idea because to weld the new metal takes time and I had a lot to do. So, I gave the car a sanding on the bare metal with 80 grit (o give the primer a good base to grip) and primed the car to prevent it from rusting up again. As I am going through, replacing what needs to be replaced and making the necessary mods, I sand back down to the metal in the areas I am welding. Once done, I shoot a quick coat of Epoxy primer over my work and move to the next piece.
Before I primed the entire car I was able to weld in a new driver's side floor pan (front and back) and put a new transmission hump in for a Keisler 5 speed. Before I took the car to the blaster, I had everything trimmed and ready to weld, so this was something easy and quick to do when I got the car back. So far in addition to the pans and hump, I have replace the drivers side rear frame rail, trunk floors, patched the firewall and wheel wells. I still have to install torque boxes, frame connectors, patch the tail panel, patch drivers side rear quarter, patch the area below the rear seat on the driver's side, and I am debating on replacing the passenger floor pan or patching it.
Bottom line, is that you need to evaluate how long it is going to take you to do all the metal work you plan to do, then add some time to accommodate what you didn't expect. Personally, if I wasn't able to work a straight week and get it all done, I would prime the car first and then do your metal work like I have done. Rust starts quick and quicker in humid areas!
I have decided that when it comes to painting, I will probably paint the underside and inside of the car before I start my actual outside body work. I have already painted the engine compartment and still have the above tasks to complete. I don't see any issue with masking these areas off when moving to the next section.
The pedals for a manual bolt in just like the automatic's do.
I don't know if any of this is helpful, but it is what I am doing and you should know this is my first time doing all of this type of work. Others will probably have better ideas and experience.
