I have tried reloading the system and downloading the updates. I am giving this Mac Mini to my father-in-law and I had the same problem before reloading the system when I was trying to load the contents onto my new Mini Server. My solution at the time was to put the mini into external drive mode and use a Firewire cable to connect to the new macmini. I would really like a solution that doesn't envolve buying cables or tearing apart his old computer.
Right now I can't load Migration Assistant on my Mac Mini Server because the Migration Assistant doesn't show up despite various attempts to load it. It is part of the system, so it should be there. I have no reference to this problem because there is no discussion about it or similar problem that appears through google searching.
OS X Servers do not have Migration Assistant - this only on client computers.
If you want your father to use the OS X Server it will be a manual data transfer. It can be done over the network, external USB drive or as you mentioned various cables.