[sumguy]

Calibre's PDF conversion is awful, in particular the "Heuristics" for unwrapping text just based on line length is basically unusable. Try Mobipocket Creator instead, it does a much better job, and can be used with Sigil to make EPUBs. It's really worthwhile to learn Sigil rather than struggling with Calibre to author EPUBs.

[edit: I just learned that Calibre has a new book editor module, that's meant to provide a replacement for Sigil, which isn't being developed anymore. I haven't tried it yet, but it could be a good alternative.]

My workflow is import PDF into Mobipocket Creator, and then just quit without doing anything else. Grab the resulting HTML file & images and import into Sigil. Clean it up by hand and/or regular expressions, add table of contents and cover, etc. Much better results than Calibre, though still a lot of hand editing to do often, Mobipocket does make some irritating mistakes, particularly with links and footnotes.