Why can't you edit it with some fraction at a time?
I've found that the process of breaking a book up into "chunks" to be a useful one to me. If I can't chunk it, there's probably something wrong with the structure.
But hell, if what you have works for you, go for it. I'm currently using the LeanPub build system which seems to be just enough structure without getting in the way.
(Me? I'd use Emacs..)