AFAIK rTorrent ports can be configured in it's config file (as you already seem aware).
Webmin is hidden behind stunnel so you can adjust that port in /etc/stunnel/stunnel.conf
ruTorrent (rTorrent web interface) is served by nginx so if you want to adjust it's port then edit /etc/nginx/sites-available/rutorrent (not that you asked just thought I'd add that!)
Should be easy to change rtorrent ports