I can't answer why the backup didn't work, but I can tell you that you want the OmniFocus.ofocus file from your old <user>/Library/Application Support/OmniFocus directory. The OmniFocusDatabase2 file is a cache of the information in the OmniFocus.ofocus file for efficiency, and is not the primary storage location.
There's no option to have the notes displayed separately like there is in OmniOutliner. To make a feature request, use Help->Send Feedback or send email to
omnifocus@omnigroup.com.