I'll leave out all the bolt on part details, I'll just discuss body color painted parts only here.
Bolt on the doors, fenders, hood hinges, hood, and header panel. Before bolting on the fenders, don't forget the strip of seam sealer that goes between the upper fenders and the upper inner fenders as it gets painted over as well, add any seam sealer around the hood hinges and other areas (look at original cars for reference as to where). Now, align ALL of the componants to thier final adjusted location, this is critical as once painted you can't adjust anything without ruining your paint finish on attaching hardware and seam sealer. From the factory all of the nuts and bolts the hold the sheet metal on the car were painted along with the rest of the car which is why adjusting them is a problem after paint, cracked paint will surely be the outcome if you start turning bolts to adjust sheet metal after paint.
The front and rear valance panels were painted off the car and added after paint so those can be left off for now, but be sure to paint it all at the same time or you could have shade differences when it's all assembled. Obviously thier attaching hardware does not get painted. I like to have the front and rear valances sprayed suspended in the same direction as if bolted to the car to get any metal flake flowing in the same direction as the rest of the car.
Once you have the front sheet metal all bolted up and aligned properly it's time to spray it all body color. The factory did a poor job of painting underneath the panels, 90% of thier surfaces usually remained in primer/sealer, and for an OE restoration this is the way to leave them, but for most purposes it's a good idea to paint all of the undersides while the parts are off the car prior to assembly.
Once you have everything painted you can add the other bolt componants which are a mixture of bare metal, Cosmoline coated cast iron, and various shades of black painted parts such as the K-member. BTW, the camber bolts and washers DID NOT get any body paint, they were black phosphate, I can't begin to tell you how many painters paint these body color! They really stick out like a sore thumb on an otherwise correct looking under hood restoration.
Hope this helped a bit,
Good luck!