Hello and welcome !! You are getting an answer from some one that put such time into a restoration finished in 2010 (9 years actually).
It is good that you got the AMK book, it has to be used in conjunction with a set of 1969 assembly manuals and examples of HARDWARE used on your car!
You will find that none of the book take into account factory hardware differences. Reading that you have a Dearborn car/going restomod will make it easier.
On the finishes (again this is plant specific) BUT there is much to be garnered from searching sites like this, 428CJ.org and Boss302.com . Expect to spend hours looking at photos in galleries of cars, learning how to "only look at original examples"/cars like yours.
When I did my car there wasn't as much info as there is today. Efforts like Marcus's
http://www.anghelrestorations.com/mustang-factoids.html as well as the MANY members that will help if you ask make car building/restoration fun.
(Not just for you, but for all) I strongly suggest that you/we include our location, car condition and "planned direction" on intros !! SO OFTEN I read and see I have an item or can help but don't know if the member is near me - or more importantly WHERE THEY ARE - as I often find after the fact I was near them on a car trip! This is important from both a logistics standpoint (read when someone needs a block 2000 miles away) and from the ability to suggest assistance from another.
Again welcome and congratulations on making the call to build a car.
Mark
P.S. I go to ROY'S CHICKEN in OK for lunch 1/15/2016 if you need parts delivered ! LOL