Lifehacker has an article HERE on how to convert pdf to epub, you can probably dig up a few more with a quicker google search (And work's kinda weird about what it sites you can access, so I can't check how easy this one is to do)
Having tested Calibre (admittedly only for a short while) while it does render a functional epub, it's quite disorganized.
Personally I convert with mobipocket creator to get html\mobi. I have a routine to run to clean it up and it fixes the majority of the issues.Interestingly enough, I think I can note when an editor changes things. Portions of the book just convert differently.
By the way, what is Shadows of Faith about? Is it the start of the Jihad and when will we get novels dealing with that event?
Would you mind outlining that process over in this thread? I am trying to get info on eReaders collected and a good workflow would be nice to add.
Further question: what part of Shadows of Faith is not published in the Dawn of the Jihad/Blake Ascending? I thought most of SoF was in the opening pages of DotJ, in the section titled (appropriately enough) "Shadows of Faith."