I can't say for sure on the bottom of the hood, but regarding other areas:
Previous to the exterior color being applied at the factory:
-Doors were installed with no internals, just the bare door shells
-Trunk lid and hinges were installed, but your Shelby would have had the trunk lid added at AO Smith, so the bolts that attach are not painted. The striker hardware was not installed prior to paint.
-Rear valence was installed but the bottom corners not attached. This means the rear bumperette brackets that attach behind the valence would have been installed. They would be painted black and could possibly have a little body color speckling from painting, but usually not much.
You are correct on the front fender brackets, they were installed after the car was painted, but prior to the fenders going on.
There are lots of little details to contend with concerning the Shelby fiberglass parts, so keep that in mind when going forward. From your current perspective, though, it is best to concentrate on how the car would have been built at Metuchen and then worry about the Shelby-unique additions later.