No experience in the way you are doing it, but it sounds like you need an OCR solution that preserves layout. Using key words in that regard may help you find something.

If you also want a project, this site looks to be a good resource on building a book scanning rig: http://www.diybookscanner.org . They also have some forums, and some of the software discussion there may interest you.

All of my ebook experience has been using already digitized text sources and using Pages or iBooks Author to save to ePub on a Mac. I know your anti Mac views, but I figured I'd mention those two apps for others here.