Nano /mnt/zfs1/jails/owncloud_1/usr/pbi/owncloud-amd64/etc/apache22/extra/httpd-ssl.conf
Edit all instants of 443 to new port number.
Line:Text --------- 35:# Listen directives: "Listen [::]:443" and "Listen 0.0.0.0:443" 37:Listen 5443 74:<VirtualHost _default_:5443> 78:ServerName www.example.com:5443
Restart OwnCloud by going to FreeNAS web gui, clicking Plugins along the top, and switching the Owncloud service off then on again.