Just do everything by hand, since that's what you seem to want, why bother having any software in the way?
If all you want is a converter, make a little batch file to _just_ do simple conversions without starting the whole app. There's also "hampstersoft"?'s ebook front end for calibre, tho it looks... ugh, it is meant to be for simple folk.
lastly:
http://alternativeto.net/software/calibre/