Ebooks

Hey, guys. I've successfully used EpubMerge before, but I tried it again today and wasn't too happy with the results. Here were the issues I encountered:

1. Calibre generated its own cover for each of the books in the series. I created a cover for the entire series, but I don't want the individual books to have their own covers. Is there a way to tell Calibre that you only want one cover for the series?

2. There's no table of contents at the beginning, listing each part of the series. Is there any way to add that?

3. In the table of contents at the back of the series, each individual book had two "chapters" listed under it: the author's name, and the author's notes. (Probably relevant: I downloaded the series from Archive of Our Own.) Is there any way to remove that? Obviously I would want the actual chapters, if each individual book was a multi-chapter fic; but since that's not the case, I don't want the author and author's notes to count as chapters.

On a separate note, has anyone ever had trouble with their covers transferring to the Kindle Fire? I use the "Send to Kindle Fire" plug-in thing that Amazon offers, because it sends all my fics to "Docs" instead of "Books" (don't want random people noticing my fanfic, lol). But half the time I use the plug-in, the covers don't transfer and I get a generic white cover with black text.

Any help with any of these issues would be greatly appreciated! =)