Time for a bit of a follow up on my server name issues with TFS. As expected there is correct way to alter the names of the various TFS servers, it involves editing the contents of one of the TFS database tables, not any config file.
The best documentation I have found is that for setting up the new ISAPI filter provided with TFS Service Pack 1 to assist in authentication. Have a look at http://msdn2.microsoft.com/en-gb/library/aa833872(… the section ISAPI does detail how to alter the names in various locations.
Though I have this ISAPI filter in place I still do not have Internet access to reports or documents in Team Explorer outside my office (though they work in a browser), I still get the small red crosses, but I am still looking for a solution. More later I am sure.