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i think i'll convert everything to rtf, fix them, and store them. then, once i figue out which format works best on my reader, i can convert from there. rtf is an easy and intuitive format for me - i'm no good at scripts!
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For some reason I've found that Calibre seems to convert better from html than rtf, so if you're converting a bunch to your preferred standards, I'd save them as html.
Now, I'm not sure if you've tried this much, but Calibre does a pretty good job of fixing a lot of the formating problems with books if you tell it to convert to epub, and tweak the settings to your liking (for instance, I tell it to remove extra lines after paragraph and add a 1.5 em indentation to each paragraph). This can be a great first step for the epub editing. After that, I've quite liked using
Sigil to tweak the books into the perfect formatting.