Just some observations here -
An eBook PDF ought to be a well-formed Tagged PDF. Why? One purpose of Tagged PDF is the support of reflow on mobile devices.
Once a Tagged output PDF is made you would want Acrobat Pro so you could review/edit the Tagged PDF's structure tree to assure the PDF has no "rough edges".
To produce the Tagged output PDF you would want an authoring application that has adequate tag management associated with it.
Such authoring applications could be:
--| Adobe FrameMaker
--| Adobe InDesign
--| MS Word
--| Open Office
Regarding MS Word - The PDFMaker that is provided by install of Acrobat provides the means of producing a Tagged output PDF.
For Office 2007 there is a Microsoft add-in that can be used; or, for Office 2010 this feature is built-in.
Important to remember is the proper use of the authoring application's built-in Headings / Styles / Paragraph/Character Tags.
Mastering content with the authoring application needs to be done in a manner that establishes an underlying logical hierarchy for the flow of content.
Because Tagged output PDF also supports Accessibility there are discussions of how to author and how to finalize (with Acrobat Pro) for Accessible PDF out on the web. If you produce a well-formed Tagged PDF that is Accessible (easy to use with Assistive Technology applications) you will also have a good PDF for use on mobile devices.
You may want to consider using a smaller page size in the authoring application such as something like 5 inches by 7 inches.
Most eBook readers available today can "read" read unprotected PDF files. "Protected" PDF (Digital Rights Management or DRM applied makes the file "protected") typically come from publishers who use the Adobe DRM services. Most eReaders, in conjunction with Adobe Digital Editions, can "read" these.
But, to apply effective DRM is not inexpensive so you may have to consider providing unprotected eBook PDFs.
An alternative (if "protected" is important but "Publisher" grade DRM is too expensive) might be to use Adobe InDesign and Calibre to develop the format that can be provided to the Amazon process for output to the Kindle format of eBook.