Most configuration files have comments explaining what you can tweak, and what they can help with, so I encourage you to go through those.
Janus can run as whatever user you want: it doesn't need root permissions at all, and I always run it with my own user for instance. Of course, this only works as long as it has read/write permissions where needed (e.g., to parse config files and update them when requested, or to save recordings).
As to the media ports, that depends. The less ports you open, the less PeerConnections you'll be able to have active at the same time, as each PC will need its own port for exchanging media with the peer.
Not planning on working on the documents you suggested, sorry: we're busy enough as we are, and that's a very generic title for what can have a ton of different approaches and solutions. Different plugins may have different requirements (e.g., how do I make sure only some people can create a room?), and so do different transports. We have different authentication mechanisms as well. Again, going through the configuration options is the easiest way to figure out this stuff.
L.