For all of our Linux machines we normally log in as a sudo/wheel user and sudo where needed
When I log in as root I do not get errors but if I log in with my user credentials (cjacobsen) I get the PHP errors "at login".
On my FreePBX asterisk 11 machine logging as cjacobsen I do not get errors so I assume that in the new distro I also should not get errors.
I ran the fwconsole chown as root
I am not sure what you mean by remove the motd file manually