A reasonably busy webmin forum:
http://webmin.us/
Log Files in some Virtualmin install:
/var/log/virtualmin
PHP (php.ini) - at some point Virtualmin gained the ability to have separate php.ini files for each VS in /home/[vs]/etc/php5
.
https://www.virtualmin.com/documentation/webdev/php
Let's Encrypt - Virtualmin > Server Configuration > SSL Certificate > Let's Encrypt