As for the question about the awkward reading experience with a two layered pdf file, there is certainly the option of converting the initial pdf file to an epub via html.
While gaining a nice text flow, there is, however, a drawback: one would lose the ability to verify the converted text by comparing it to the original (in case there have been errors during the conversion process). Anyhow, to do this in one title or one file would be, I think, quite nice.
Even more important is, to my mind, the fact that with the epub file there also goes the ability to cite the right page number – and that is something I consider, for my rather academic purposes, as quite important. Especially if I highlight some passages of the text, take notes and, eventually, export them via Reader Library. Then, in particular, the epub should take into account the many peculiar exceptions, i.e. the Roman numeral page numbers of a preface or the articles that begin at p. 137 and not at p. 1.
But perhaps there is a solution to this problem that I haven’t seen.
Last edited by wonderose; 04-25-2011 at 05:43 PM.