You can set default font sizes or give it a default CSS stylesheet and then reconvert ePubs so that they'll use those settings. And since you're doing that to the existing ePub, you'll keep your TOC. It does batch converts, too.
(ISTR that that Reader wouldn't let you sort by author last name by default, which Calibre will also let you do (if it doesn't do it by default, then preferences/advanced/plugins/device interface plugins/Sony/Customize Plugin/"use author sort for author"). That alone made it worth using Calibre for me.)
For the heavy indents, it probably depends on how they're doing it. If it's CSS, you can override it with Calibre's conversion settings. Or if you need to edit as RTF, you can save as HTML and open in Sigil, http://code.google.com/p/sigil/ , which will create TOC links for things that are HTML headings (H1, H2, etc.) and then you can re-save as ePub. I do a lot of home-rolled e-books (downloaded fanfic) and use Sigil for that. (Calibre also autodetects HTML headings as TOC links, but last I tried it didn't do them hierarchically, which Sigil can.)
no subject
You can set default font sizes or give it a default CSS stylesheet and then reconvert ePubs so that they'll use those settings. And since you're doing that to the existing ePub, you'll keep your TOC. It does batch converts, too.
(ISTR that that Reader wouldn't let you sort by author last name by default, which Calibre will also let you do (if it doesn't do it by default, then preferences/advanced/plugins/device interface plugins/Sony/Customize Plugin/"use author sort for author"). That alone made it worth using Calibre for me.)
For the heavy indents, it probably depends on how they're doing it. If it's CSS, you can override it with Calibre's conversion settings. Or if you need to edit as RTF, you can save as HTML and open in Sigil, http://code.google.com/p/sigil/ , which will create TOC links for things that are HTML headings (H1, H2, etc.) and then you can re-save as ePub. I do a lot of home-rolled e-books (downloaded fanfic) and use Sigil for that. (Calibre also autodetects HTML headings as TOC links, but last I tried it didn't do them hierarchically, which Sigil can.)