ISPConfig 3 has two different configuration files, one for the server part and one for the interface.
ISPConfig 3 Interface
The config file location is:
/usr/local/ispconfig/interface/lib/config.inc.php
ISPConfig 3 Server
The config file location is:
/usr/local/ispconfig/server/lib/config.inc.php
The MySQL root password that is used to create new MySQL databases only is stored in the file:
/usr/local/ispconfig/server/lib/mysql_clientdb.conf
