Spent some more time looking at the structure of the Yakubun document. In particular, I noticed that there seem to be no anchors linking endnotes to the position in the text where they actually appear, making it impossible to insert a note marker (or the note itself, if we're using TEI or something similar) in the right place in the text. Wrote to DB to ask about this, and also to ask in a more general sense what his plans are for editing the documents in the future. I think it might be hopeless, and pointless, to try to reproduce much of the original formatting, given that it's often repetitive low-level stuff that ought to be done globally anyway, in most document formats, and much of it will be irrelevant outside the context of the original printer.