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You have a few options for editing the file. I'd say the easiest way is to use Sigil to open the ePub directly and edit there. You can also add TOC entries prety easily. There are other ways as well, such as using an editor like eCub, Adobe InDesign ($$) all the way to editing the HTML directly. Take a look in this forum, you'll find a few threads talking about the different ways of editing.
For this type of conversion, the automatic tools can't get you all the way there. I'd say start with Sigil and see how that suits you. It's free and pretty easy to use.
- Ed
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