Depending upon how far they are stripped and what work is done to the window frames the doors will be a pain, and though helpful, you'll find no matter what you do prior to paint they'll still need a lot of work on final assembly.
I assume you checked them prior to disassembly? I cant remember what state your car was when you bought it.
I'd advise new phosphor-bronze hinge bushes as a bare minimum. And do nothing until they are fitted into the door beams.
If you have marked the position of the window frame and check strap attachment points ie. the angles and position along the beam, that will be your biggest advantage. I had put in a light score mark on my beams for this purpose.
Though a more thorough and professional finish, I'm not sure I'd recommend powder coating your window frames due to the effort it takes to refit the quarterlight glass. And given it's relatively rarity (on an S1 at least), the danger of damage during that process.
Depending upon how far you intend to disassemble the doors there is little benefit from marking the penny washer shims, though all information is useful at the end of the day, as an indication at least. You'll find you'll have to start from first principals. A seemingly endless task. So to recap do that after you've fitted those bushes. Not the original plastic type which won't last.
Contrary to other comments about door SJ Sportcars' door rubbers, I have not found them a problem. Like any new rubber they just need careful banging into place and adjustment of the window frames afterwards. I noted that the S1 featured on the recent Top Gear programme leaked from the tops of the doors. That car would benefit from some attention in the door frame angle. Which will mean more than adjusting with the penny washer shims. Mine took a little effort to get right. Patience is a virtue in these circumstances.
I'm also not sure of the worth in spending time on the bonnet and rear hatch, but the lamp pods may benefit from a test fit.
Overall, better off spending time progressing the other parts of the restoration. Heater box, steering, suspension, interior panels, and gearchange linkages etc. It is a momentus task to completely rebuild these cars without wasting time on stuff you'll need to redo once painted anyway.
I hope that helps.