Yes Will, I have tried that, just before I did read your input :) .
Unfortunately I was not able to fulfill the task due to errors like:
failed to enumerate objects in the container ... Access denied.
I could see that the files giving errors are new files from the upgrade and these files has the "owner" = the specified application pool.
When I try to update the permissions I am logged in as admin user on the server via a remote desktop. All older files has "owner" = the admin user, same as I was using when I when I was working on the server.
Perhaps I need to change the "owner" of ALL files in the website folder to the admin user, before I try to change the permissions?
I do not know how to do that. Can you help me out?
All the best!