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There's a lot of negativity for pdfs here (which is understandable), but for those of us who need long and difficult equations, really there's no other formant available besides latex to pdf or postscript. Epub and mobi just don't support complicated equations.
Anyway, back to the question at hand, do you really need to convert your pdf to ebook format? I've managed to get along quite well by cropping pages, adding bookmarks, etc. There are a lot of tools out there for manipulating pdfs. I think learning to live with pdfs on your ereader might be less frustrating than trying to convert it.
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