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Yeah, the problem is indeed the way a given PDF is output.
In general the problem is so hard, that starting from scratch (sometimes even the plain text cannot be copied properly!) is the best way to go.
(Not to mention the embarassing number of "Conversion services! For cheap! Any language, Groundhoggese included! PDF to EPUB3!" which create EPUBs which are a sequence of images inside an EPUB3 container (!) or they use stuff like pdf2htmlEX to get a "sort of EPUB3 FXL, but you need Javascript to actually see it"...)
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