Scanning

Dual cameras: Hardware Trigger
When you use a hardware trigger, all the even pages will be on one camera and the odd pages will be on the other. In order to merge them together, you must first check that all the pages are accounted for, then rename them to odd or even.

These two bash scripts (Mac/Linux) can be used to do the renaming. After you rename, you just move them to one folder for scantailor to process.

Scantailor
Finally, after the odd and even pages are collated into one folder, you're ready to use Scantailor. (Can be found in Debian and Fedora repos)

http://scantailor.org/

Notice that Scantailor outputs to .tif in the out/ folder. You will need to use tiffcp to combine them, and tiff2pdf to turn it into an actual pdf file.

http://www.moreno.marzolla.name/software/scan-to-pdf/