The Windows Server Update Services on Windows Server 2012 R2 base install of the role errors after basic options are specified. The SQL Server database has indexes missing causing timeout errors. It is also important to not check the download of drivers as this will fill up your drive.
Powershell script to add indexes to the database and removes deprecated updates.
Download for Clean-WSUS.ps1 powershell script: https://community.spiceworks.com/scripts/show/2998-adamj-clean-wsus