I honestly fail to see the need for a single monolithic HTML file, but your mileage may vary. EPub is, as far as ebook formats go, the most versatile format as far as formatting goes, as well as being the easiest to manage with Calibre, since most of the times, no conversion is needed in order for the metadata to be correct when I export a file. The first reason is why I suggested it here- if you have a base format preserving much, if not all, of the layout, you can expect pretty good conversion results.
Oh, and did I mention there's a
WYSIWYG editor available, as well?