I think issues 1, 5, 6, 7, 8, and 9 could all be eliminated by making a small modification to the procedure. For a measurer submitting electronic versions of his maps, the state certifier does not send in paper versions to the registrar. Instead, he sends the certificate and map to the measurer(which he does already). The measurer scans in the certificate and sends that to the registrar along with his electronic map.
This eliminates all the scanning issues mentioned, and also eliminates any confusion, because the electronic version is the only one the registrar ever sees.