You can use LaTeX (a typesetting language) together with a version control system. You could split up your document across multiple files and have a main document which references all these subdocuments. I've been using LaTeX since I started university to write all my reports, and I've never had to deal with infuriating Word formatting problems and inconsistencies ever again.

For example, check out http://en.wikibooks.org/wiki/LaTeX/Tables to see just how easy it is to clearly define exactly what you want!

Your use case sounds perfect for LaTeX!