The bottom line on the current situation is that the 2 eBook formats to focus on are PDF and ePub.  PDF will cover Kindle, and ePub will cover pretty much everything else.

Sigil: ePub format native editor
http://code.google.com/p/sigil/

Calibre: ePub file converter and eBook reader:
http://calibre-ebook.com/

Calibre is going to show you the format of your book in the ePub format after a PDF > to ePub conversion.

Sigil is going to be where you are going to edit the ePub file into it’s final format

1. Download the 2 applications
2. Install the applications on her PC
3. Translate your book from PDF to ePub format
4. Open the translated ePub format version of  your book in Sigil and Calibre
5. Calibre will show you the format of your book in the ePub format eReader
6. Sigil is going to be where you are going to edit the ePub file into it’s final format
7. Start the editing process in Sigil, saving to a new version as you go.
8. Be sure to save your working file in a new version number to avoid confusion.

Comparison of e-book formats:
http://en.wikipedia.org/wiki/Comparison_of_e-book_formats

Comparison of e-book readers:
http://en.wikipedia.org/wiki/Comparison_of_e-book_readers

How Can I Convert PDFs and Other Ebooks to the ePub Format?:
http://lifehacker.com/#!5509965/how-can-i-convert-pdfs-and-other-ebooks-to-the-epub-format

Giz Explains: How You’re Gonna Get Screwed By Ebook Formats:
http://gizmodo.com/#!5478842/giz-explains-how-youre-gonna-get-screwed-by-ebook-formats

Kindle Native Formats:

The original Kindle supported only unprotected Mobipocket books (MOBI, PRC), plain text files (TXT), Topaz format books (TPZ), and Amazon’s proprietary DRM-restricted format (AZW). Version 2.3 firmware upgrade for Kindle 2 (U.S. and International) added native Portable Document Format (PDF) support. Earlier versions did not fully support PDF, but Amazon provided “experimental” conversion to the native AZW format, with the caveat that not all PDFs may format correctly. It does not support the EPUB ebook standard. However there is software available (e.g. Calibre) which can convert a non-DRM EPUB file into the unprotected Mobipocket format that the Kindle can read. Amazon offers an email-based service that will convert JPEG, GIF, PNG and BMP graphics to AZW.

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