I don't think that there is any current automated system that will help you.
Yes, ePub3 is supposed to support MathML, but
(a) few readers support the full ePub 3 spec (non yet fully support the ePub 2 spec!)
(b) PDFs are glyphs on a plane if you're lucky (if unlucky, just bitmaps). There's usually no semantic mark-up that would help convert the equations to MathsML.
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