Hi there!
First of all, huge props for this most awesome bit of software!
I am running PlexConnect on an Ubuntu Linux server, which also hosts my DHCP and DNS services for the home network.
I have bind9 working for my purposes, but I'm not much of a guru with it, and I couldn't get it to do what's needed without breaking all *.apple.com requests.
So I attempted to get the PlexConnect DNS component working alongside bind9, which turned out to be quite simple.
First, I added a second IP address in /etc/networking/interfaces, which would be for PlexConnect's DNS only.
Next, I edited named.conf.options, to force bind9 to only listen on the original IP and 127.0.0.1.
Finally, I edited DNSServer.py to force that script to only listen on the new IP:
Changed line 313:
DNS.bind(('',53))
to
DNS.bind(('192.168.15.243',53))
Clearly, hardcoding the IP address is not ideal, it should be a variable of some sort, but this was my quick-and-dirty solution to get it up and running.
I don't think there needs to be a change to PlexConnect, I think I have a fairly edge case here. Just thought I'd share my solution. :)