Hello everyone I got this problem solved. There was two areas that did not auto set in the installation. I am not sure if the installation build up of the Application server should do this or not, but here is what I had to do to fix this error.
In IIS I had to verify Windows Authentication was enabled for the web site being used. It was set to “disabled”. Once I enabled this this it worked fine for logging into the system with single sign-on.
Secondly, once the certificate is created in the admin console. You need to ensure it is correctly loaded into the Trusted locations. Once this is done the application server build out can successfully load it into the database. This will also allow the REST services page to come up properly on the server. Once this cert is loaded on the client then the REST services help page will come up without error there too.
Thanks for the comments! I hope this helps someone as well.