I didn’t have any of these issue(s) fortunately… I also rebuilt the site literally 20 times on Windows 2012 and Windows 2016. I also installed it to C:\inetpub and D:\Websites (custom folder) without a problem.
I also did it under a User that has Local Admin Privileges. I also used the Custom Account option in the App Server config and pointed it to sa-epicor (service account)
It is actually a simple issue as this happened to me as well. It mean when you started the EpicorAdmin Console, you did not start it with elevated privileges. Just right-click and choose “Run as administrator” when opening the admin console. This issue will be no more