1. I get the error "No ACL setup yet! Denying access to everyone." on the login screen
Show us your ACLs. You probably miss a rule for @ALL on the root.
2. AD NTLM SSO does not work anymore. Users are presented with the logon screen with the purple "No ACL setup yet! Denying access to everyone." Users can enter their credentials and log on fine.
I have the old server up and running and have been comparing IIS and PHP configurations. Other than version differences the configurations are very similar.
Hard to give any advice here without knowing your exact setup.