What I've been doing the is either:
1 - open the PDF in MobiPocket Creator and take the resulting HTML file and pop it into Word. Then I basically mark everything as normal text, ditch any smarttags, remove xml tags/template, re-format paragraphs and headings and then save as either .doc or filtered .html and then use MobiPocket Creator to make my .mobi file
2 - Use Abbyy PDF Transform to get a .doc or .rtf file out and then do same editing and formatting as above.
Both of these are painful to do...paragraphs broken in the middle of sentences, spacing/punctuation errors, etc. But I am pretty picky and spending the time doing this gives me a pretty good .mobi file.
Once everything is .mobi it goes in my library and moved to my Kindle.
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