Most of that delayed time from the server upgrade has been spent reorganizing the main NAS data (and changing the system drive and backup drive). So I finally wrangled that issue.

The WD WD10EALS 1TB scratch disk is officially retired, as attempting to write data normally past the 139GB barrier actually crashes the drive and it would return as unrecognized. This did not show up in either the HD Tune Pro verify scan or the MHDD scan. (This, however, did hang HD Tune Pro, but the drive would return a few minutes later and the scan would resume as if nothing had happened.) The unrecognized part only happens when writing data normally.

Amusingly, this also did not show up in the HD Tune Pro erase procedure, but a verify after that would mark that area as red, but not crash the drive.