My preferred way would be to make the port static on the server with the named instance.

You would do this by choosing a port not in use on the server as well as a port that is not a standard port for any other service or program. You would not want to use 3389(rdp), 443(ssl), 3306(MySQL). Here is a list of standard ports (http://en.wikipedia.org/wiki/List_of_TCP_and_UDP_port_numbers)

Enter whatever port you choose into the TCP Port field for the IP of the server.(http://support.microsoft.com/kb/823938) you will need to restart SQL Server for the change to take effect.

If you do this you can then create an alias in "SQL Native Client Configuration" in configuration manager on the source server point to the servername and port and create your linked server with just the alias name.

other option is to get SQL Browser working between the servers and then you don't have to give the named instance a static IP and you could use SERVERNAME/INSTANCE for your linked server.