Got some basic layout styles done, and then added the note and reference popup code. The way I've done it means that if JavaScript is turned off, note and reference links simply bounce you to the bottom of the page (or the appropriate place); if JS is on, then the href attribute is removed, and an onclick event pops up the relevant info in the right margin. This is basically working, except for some types of link (internal links to tables, appendices etc.), which need to be looked at.

But we're nearly there for the XHTML!