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Actually, for my own use I like the Calibre conversion somewhat better. But for commercial applications (Kindle store) I pretty much have to go with kindlegen starting with a "specially crafted" epub to get the results I want. Which is why I'm a little hazy on the details of Calibre conversions.
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I'm the same way. But if it's not strictly for personal use I've taken to:
1) Converting the epub to mobi with calibre
2) unpacking that mobi with mobiunpack.py
3) recreating the toc.ncx and tweaking the opf file by hand (I also have a few automated scripts of my own to help)
4) feeding the opf file to kindlegen
I get the look of the calibre conversion, but produced by kindlegen.