In your picture 1, electrical components are not usually shown in the Interior Assembly Manual .
In your picture 3, the wire retainer is part of the wiring harness.
In your picture 9, the staples for the insulation and the insulation are part of a subassembly so they would not be in the Interior Assembly Manual.
In your picture 10, the screw shown appears to be longer than the 7/8 screw specified.
In your picture 11, the wafer head screws are probably the same ones, 380858-S2, used to attach the side rail weatherstrip. (A side note, Ford may have gone to drill tip screws to eliminate a drilling step, so these may be that same drill tip type. there is a difference in that the weatherstrip uses a 10-16 and the AMK Guide only has a 8-18 size listed.)
In your picture 12, the pan head screws appear to be as called out, the washers are not. I would consider the use of the washers to be a better method as their use provides a larger "footprint" for attaching the console to the bracket.
Jim