I suggest that you get a set of the 65 Mustang Assembly Manuals by Osborn Reproductions; Body, Interior, Electrical, Engine Accessories, and the 64-65 Chassis and the 64-65 Weld & Sealant Manuals. A good deal of your questions are answered there, especially the hardware finish, engine compartment finish, assembly order and window alignment. They are about 90 to 95 percent accurate but give you a reference that many of us can use to assist you in your project.
Jim