On the way home from work yesterday I decided I was going to take apart one of my vintage Yamaha guitars to become a neck joint demo. A 1973 FG-200. It was an ugly guitar I got cheap and it became my first vintage Yamaha neck reset nearly 3 years ago. First step, take it apart!! Neck off, removed truss rod, tuners, pickguard & bridge. The next step is to fit the neck joint back together (slip fit, not glued) after it's a day to dry after steaming it apart. Then cut out a rectangular section of the body and support the sides with some 1/2" maple. And cut the neck off, I think between the 9th & 10th frets. I won't cut the vintage truss rod, I'll make a fake one, just to add that level of detail.
These pictures show (at least for this model) the back plywood is ALL mahogany, The side plywood is some kind of white wood (probably spruce) sandwiched between 2 layers of mahogany, And the top plywood is 3 layers of spruce.