I think that MS has very good tools for XML generation and editing. Isn't there a utility for going between Word and XML? XML has the depth of the book organization but allows for the easy manipulation by Perl and many other tools.
I'm talking off the top of my head here, and would be hard put to give a demonstration, but this is something I would investigate if I were to do another book or more book scale editing.
What is STM books?
I found this commercial suite of products
for doing the conversions between Word and XML.