If you're using Window, then PDFzilla - a program for converting PDFs to a variety of (non-eBook) formats - is available free until 5 February 2011. If nothing else, it will give you a "second opinion" on how well your PDF can be converted.
I haven't tried the program yet, but what I've got in mind is to convert a source PDF to an interim format (say RTF) where I can tidy up and/or edit the document, and then convert the interim format to an eBook format using Calibre.
If you're interested, have a look at
http://www.pdfzilla.com.