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LaaurenTaaylor if you use Windows:-
Then, if ever you have a pdf which Calibre doesn't convert satisfactorily, try using the MobiCreator tool - there's a link in the "Read this ..." sticky.
It creates a PRC which you can then Calibre convert to Epub, Mobi etc. My experience is that it normally does a better job than Calibre at PDF conversions. And because PRC is 'more-or-less' the same as MOBI, then Calibre should convert PRC very 'faithfully' to your preferred target format.
Don't look for any 'tweaks' in MobiCreator, there are none, apart from output destination and a couple of other such settings. I think there's a How To Use video on YouTube.
BR