I bet you'll find that no data structure of this world will be able to represent thoughts or life and you'll be making compromises. As time goes on, the compromises accumulate and you'll star to see less value in what you are doing. Not to discourage you, but I've tried similar things e.g. when I started http://madduck.net in 1996 (which I took offline in 1999), using links between pages and thought I could put my life online...
I think this is a great idea and I can't wait to clone your book :-)
I've just finished writing a Freeform (or Theatre style) LARP using mercurial so that I can use hgtk to check the consistency in changesets. I love the idea of using distributed SCM's for writing prose instead code. The only thing is how should paragraph/sentences be order across lines. My current view is each sentence should be one line, adn a blank line for a paragraph break so that diff's can be more easily read.
While I hack on code every now and then (and mostly in very kludgey sorts of ways), I'm mostly a writer of prose. I use git to store and manage the text that I write, but I've never seriously thought about using git as a publishing too. Mostly because I think that it would limit the possibilities of who would have the expertise to read said-story. Except that Ikiwiki seems like a good possible front end (with some tweaks) and I saw a guy who used the RSS feed and community features of github to basically do a blog in readme.md files... In any case, I'm interested in seeing what you come up with.