How are you connecting to the server to administrate it? Do you use SSH over TOR? ||Home (TOR)|| > ||Server (SSH)||
Are you using Firefox to tunnel your internet activity?
He only need one ssh connection to the server and then use the remote just as standalone pc to do all Joe's jobs. The only connection from his own computer to anything which has anything to do with Joe, is that single ssh connection to that server throught tor. And after what you told, it is most likely made directly with the IP address.
Ie; rent a server in a cloud, install linux and X2Go or freeNX or whatever, then never do anything as Joe anywhere else but by using that computer on the cloud.
But he has to pay for DNS and the server. Can these payments be tracked?