vCenter Converter to migrate SME? one of the main advantage in using SME (and many other linux flavours) is that you'd never have to clone/convert the physical machine to move to a virtual one.. don't follow the windows way, use the force
Adam.. using the backup/restore function to migrate your server you will move only users, their data, and configuration dbs..
so you will not move any other info, i.e. no unwanted contribs will be installed on the new server..
you are using the wrong approach IMVHO, so yes, I see many potential issues with your method
anyway, using the "clone" method (see my wiki link above) you can customize your include/exclude list to move only the data of your preferred users.. anyway, passwd/shadow will be identical before and after the migration