I unfortunately do not have much to add by way of recommendations for software to use. However, one extreme painpoint for me as a consumer of eBooks is PDF. PDF documents are bad enough when trying to read them on a full computer monitor; on a Kindle or a Nook they are nearly unreadable, and on smartphones they are a complete non-starter (for me, at least). I would strongly encourage you to focus on formats that can be dynamically be resized based on the viewing area (e.g. ePub or Mobipocket) rather than PDF.