I followed their travels online during that year on a nearly-daily basis. A map that shows their routes in detail (although it gets a bit tangled and crowded in the most popular, re-traveled areas) can be found at:
A Year in the Wilderness. Yes, they made a conscious decision not to visit the "disconnected" areas that you mentioned, feeling that it would violate their "continuous year" by exiting and re-entering the wilderness.
I also have a signed copy of the book and although I have not read it through completely, it is a great coffee table book to pick up on occasion along with my McKenzie maps.