RH9 is proved to be stable with Plesk. The new commercial version of Redhat release is Enterprise Linux. Fedora is considered to be a distribution for developers and which may include less stable software versions. (even though there is no such reported issues yet for the usage of Fedora for commercial purpose)
It would be better for you to use RH9 if you plan the installation for mission critical applications. If you plan to give the most modern software for the customers there is no harm in using Fedora.
Installing xwindow system in the server is not dangerous. But do you really need that? The xwindow system consumes a lot of resources from the server. The migration can be done through more secure and comfortable command line interface.
If you plan the xwindow system only for your migration purpose there is no need of that. You may use the scp commands for server move.
It would be better that you seek the help of a system administrator to move the data from the remote machine.