Have you tried NotaBene, a word processor designed expressly for academics? I have it installed on my computer, but use it infrequently because I write more for general audiences and don't need the academic framed layout.
For my current major book project, I'm using Chapter-by-Chapter, a Word companion that manages each chapter as a separate file, but which allows an overview of the entire document in progress [with chapter word counts] and the ability to merge it all at the end. After merging, all the chapter and footnote numbering flow thru the full document. The notion of keeping my entire book in a single file scares me to death; Chapter-by-Chapter lets me sleep at night, while keeping tabs of my overall progress.