I work for a small (less than 10 employees, total) publisher of board, card, and roleplaying games. I design books, do grunt production on others, hire freelancers, train freelancers (apparently long document production is much more of a black art to some people than I ever expected …), build ads and convention display stuff, and do some web design.

Most of my time is spent in CS4, now, with trips back to CS3 for legacy projects and touchups on stuff that freelancers with CS3 have. 

I work with elves-with-guns and giant robots and other fantastical stuff everyday, and it's awesome. 

Are the chapters distinct PDF files? If not — the entire book is one PDF — you should be able to create the hyperlinks automatically:

* Generate the TOC using InDesign's TOC feature, being sure that “Create PDF Bookmarks” is checked in the Table of Contents dialog, along with the “Include Book Documents” checkbox if you are using an InDesign book.

* Export with the “Include Bookmarks” and “Include Hyperlinks” checkboxes ticked.

In addition to Bringhurst's book, I'd also suggest reading Stop Stealing Sheep from Adobe Press, and Ellen Lupton's Thinking with Type.

Grid-wise, I like Making and Breaking the Grid.