Hi Kyle,
As the Portal is a new portal, it should not have references to the server. However, if you did not unfederate Server, it will still believe it is a federated server. You need to update server so it no longer thinks it is federated. To do this:
1. Go to https://<server machine name>:6443/arcgis/admin
2. Navigate through Security > Config
- Here you will see that it still reads 'ARCGIS_PORTAL'
3. Update this page so the 'Authentication Tier' is 'GIS_SERVER'
This should resolve the issue you are seeing and allow you to federate your server with the portal.