So what you're basically asking is where can you get free software. Hmmm... For OCR-ing, ABBYY FineReader 11 is currently the best but you could also take a look at Tesseract 3.01 (see the "User interfaces" section as well)
"Tesseract is considered one of the most accurate free software OCR engines currently available."
For layout and post-processing there's also:
- LibreOffice (for ODT files, RTF, etc) with the Writer2ePub plugin (for exporting as ePub)
- Sigil (for editing ePub files)
- Calibre (for converting various formats, including ePub to Mobi) ...
For PDF I don't know any open source software but I'm sure there are plenty. Calibre is one of them. Note that PDF is Adobe's baby, always has been. They invented it. While it was released as an open standard in 2008, Adobe Acrobat is still their sugar daddy.