Based on some editorial feedback from HM, I've reduced the size of the images on the page to 4" wide (discovering in the process that FOP 0.20.5 doesn't support content-width, but if you just set width, it does scale the content proportionately). I also increased the space between the footer top border and the text above to a quarter of an inch.

Then I tackled endnote numbers, discovering that if you set the font size, that seems to undermine the application of the vertical-align and/or baseline-shift properties, so I've left the font size for endnote numbers in the text as default, and now I have superscripting. The link is also working, although FOP's positioning of the hot area is always slightly off. I fixed a bug that was causing all in-text footnote numbers to be "1" (xsl:number never does quite what you expect). Finally, I noticed a situation in which a URL was not having zero-width wrapping spaces inserted, and it turned out to be because it starts with https, and I was crudely trapping for http://. I'm now just looking for http, which should do the job. We may have to complicate it a bit for ftp and other protocols at some stage, but you don't see them as much as you used to.

I've now added a PDF link to the document XHTML output, so all articles are available as PDF.