The design story has to start with why do a design at all? Why not just buy a production boat, or a used boat? I spent more than a year on that question as explained in the section on why a custom boat?
Although Chuck Paine is the designer of record, the final design of the boat is the sum of the design of its major components, some of which interact which each other, and others that are almost entirely independent. Yacht design and construction has evolved dramatically in the last 30 years, with much more specialization in the design and construction of each sub-system. In the process, some of the design has passed from the designer of record to the hands of the specialist. And if you've ever built anything of major scale (like a house), you know there is always a gap between what the architect draws, and what the builder eventually builds. In fairness to everyone, some of this is due to the iterative nature of the design process. Design something today, leave it overnight, and chances are you can improve it a bit tomorrow. The builder inherits the design from the architect and inevitably has the opportunity to improve on some areas, and of course to fall short of the architects vision in others.
I've broken the design section into the major components:
Hull, keel and rudder
Cockpit & Deck plan
Sail & Rig plan
Interior
Systems