Hi Cory,
What type of authentication is configured with your web adaptor? Are you using built-in authentication or is it configured with an authentication provider such as IWA?
Also, is your Server allowing administrative access through the web adaptor? You can check this in ArcGIS Server Manager > Site > Web Adaptor.
If I am understanding your post correctly, you have two web adaptors? If they are both running through the same port/site, they will need to have different names in order to work properly.
Also, if you recently upgraded to a different version of Enterprise, you will need to uninstall the old web adaptor to install the new version.
Hope this helps!