That's about how it goes. The earliest with FoMoCo labels would most likely be the closest to original fit and appearance, although there is no guarantee. Service replacement parts were not held to the same standard as assembly line parts and any leftover parts at the assembly plant would usually be destroyed.
Of all those choices, assembly line sheet metal will be the best in fit/appearance. Depending on what sections you're looking for, such as fenders or bolt on parts, I would strongly recommend to search out a parts coupe built close in production to your Shelby at San Jose. Spending $6-12k on a nice, complete coupe (I6 or V8), can be a goldmine of parts, fasteners, clips, etc... Once you're done with the coupe, it can be sold for close to what you paid... replacing OEM with repro or whatever.
Also, don't get sucked into replacing complete panels if the originals can be patched/repaired. For instance, I would patch a battery apron that had rust on the area around the battery tray and preserve the original piece as much as possible, keeping from disturbing original spot welds. Your car will appear more original this way and minimize any issues later on with value.