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Changing the formatting should be relatively simple, and only modifying the CSS could be enough (though it could be quite "obfuscated" and messy). In my ePUB files, for instance, you'd just have to add "body{text-align:justify;}" to the OEBPS/css/style.css file.
As for adding or modifying a TOC, you want to look into the NCX file.
Finally, for editing ePUB files, I advise you to use Sigil. It's still in alpha stage, but should be pretty usable.
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