Although I haven't changed the hostnames...the application registrations and the certificates for each of the servers have been toggled between using FQDN and just shortname alone. Upon recommendation that we register the applications and generate the certificates using the short hostname, I have done so and reimported the peer certificates. In addition I had the FQDN listed as the Homepage Server Name in Home Page Admin > Settings. So it was also modified to show the shortname.
I also unregistered all remote applications.
Upon rebooting both servers, the LMS Portal had no portlets configured in it. It also had no radio buttons to select public or private view. I can access the pages by directly navigating the each applications URL (CS, CM, IPM) but the portal is just wiped out. I assume that is because the portal is based on the Home Page Server Name. Is there a directory where the old site's settings were stored?