Upon running that, the hbase migrations script says no files in root directory.

HBase expects the root directory to either not exist, or to have already been initialized by hbase running a previous time. If you create a new directory for HBase using Hadoop DFS, this error will occur. Make sure the HBase root directory does not currently exist or has been initialized by a previous run of HBase. Sure fire solution is to just use Hadoop dfs to delete the HBase root and let HBase create and initialize the directory itself.

If you have many regions on your cluster and you see an error like that reported above in this sections title in your logs, see HBASE-4246 Cluster with too many regions cannot withstand some master failover scenarios.