Lots of "invalid response from" exactly like
not sure their solution of a 'rouge www ServerAlias" applies to me, but maybe...
one thing that i think might help is that the log seems to create the .well-known validation challenges all under server.eyethrees.net but then the file not founds are all .well-known directories under each vhost's domain
my 'webroot path' in /etc/letsencrypt/renewal/server.eyethrees.net.conf is /var/www/html/server.eyethrees.net,
is the comma supposed to be there? is the webroot supposed to be just /var/www/html?
thanks for all your help, btw