there are a few things that should be run as root
. you'll notice for some that it prompts for a password or states "Warning: libexec/zmsetup.pl must be run as root!".
you can change the webmail access ports like this (with the appropriate SERVERNAME):
su - zimbra
zmprov ms SERVERNAME zimbraMailPort 81
zmprov ms SERVERNAME zimbraMailSSLPort 444
tomcat restart