You may want to check the .NET version on your app pool.
I ran the setup on the new server as we are migrating all our GIS stuff to new servers. Everything seemed to install all right but then I got a 500 error on the Config page after the install.
Turns out it is an application pool setting. I had changed the DefaultAppPool setting from .NET 2.0 to 4.0 as that is how it was set on our existing production server.
Because of that, when I installed the WebAdaptor it set the .NET version to 4.0 rather than 2.0 when setting up the ArcGISWebAdaptorAppPool. As a result I got the 500 error on the Config.aspx page.
After setting the .NET version back to 2.0 for ArcGISWebAdaptorAppPool application pool, the config page would load.
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