ePubs converted with calibre come much closer to looking like the original epub I made than kindlegen seems to. But each day, I learn new ways to format my epubs so that kindlegen doesn't butcher it. Now, usually, I can make a couple of tweaks to the CSS in my source epub before I run it through kindlegen (if there isn't any crazy layouts involved) to produce the mobi. Anything so I don't have to maintain two completely separate projects for one book. I don't do a lot of graphic stuff--I'm basically only in it for the words--so I've found that the KISS method is crucial to my personal successes.
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