There is no "but" about it I'm afraid, HarryT is spot on. PDF is a problem format to convert from, end of story. There is a whole sticky dedicated to it
here. There are no "magic settings" that can be generalised. You *might* find some tweaking of the fudging in the heuristics makes *some* parts of the document look a little better, but it will likely be at the expense of readability of other parts.
The only sure fire guaranteed way is to edit and reformat the whole document manually, line by line, usually having the PDF open on one screen and your edited version on another, fixing line breaks, hyphenation issues, OCR issues, scene breaks, page breaks, ligatures, images, tables, indentation, character substitutions and all the other "issues" that PDFs can have depending on their original content and fonts chosen.
They are a nightmare. Your best bet is to buy a reader like a tablet so you can view the PDFs full size and forget about converting them. Or you can try other third party PDF converters which people report varying success with but the same caveats will apply.
Edit: dwig beat me
