I understand there are 2 batch files that need to be run to bring the repository up to 2013 UpgradeRepositories.bat and SetupRepositoryIndices.bat . The upgrade batch file bombs for me immediately looks like it may be a permissions problem. Before I go there is there something I may be missing, like what should my current directory be when I execute.
Another alternative is to use Package Management in MapAdmin ( http://servername/mapserver2013/mapadmin/login.php