I wrote a little shell script to help post-process scanned PDFs. I actually wrote it purely for improving usability on a regular computer, but it has the side-effect of making such scans very usable on ereaders as well.
It was written for Linux, but it should probably also work on BSD, Mac, and Windows with Cygwin provided you install and compile some packages.
https://github.com/Frenzie/readablepdf
All of the hard work is done by
ScanTailor. This script automates some of the pre- and post-processing you'd need to work with ScanTailor.