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There is another, very recent discussion about converting PDF to Mobi to EPUB (required to strip some of the extra scripting inside). I believe BetterRed (might be 1 R) was the user posting what she had to do and why. You might want to do an Advanced Search for posts from her about PDF in the last week within the Calibre section of the forums.
However, in general, PDF is perhaps the absolute worst source document you could have since it doesn't convert well.
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