title_body: How to convert PDF's with footnotes for Kindle?
upvoted_answer: PDFs are not designed to be converted from. They have no structure that allows Calibre to determine for sure how many columns of text it has or what's a footnote. The Calibre manual describes the topic in more depth.
  I found that copying the text to a text editor, cleaning it up and then pasting it into the Calibre e-book editor gives the best results but it takes long and is boring.  I've written down my work-flow in a blog post. It describes how to make EPUBs, but I'm sure it can be adapted to mobi fairly easily, since it seems to use XHTML too.