No problem here, but I could some advice. With 2500 footnotes, and a similar number of links, some glossary references, and a felt need to jump to the next figure or table, I devised my own system for navigating a 25-chapter html book. The question is, will others find my system easy and understandable.
http://www.electromontis.net/evoligion/_A/Quirks.shtml explains the approach and lets one practice.
Footnotes haven't received much attention from W3C, so one has to improvize. Suggestions appreciated.