I've successfully installed Plexconnect on my AppleTV 3 running v 5.2.1 from the latest Github archive - i.e. the one which includes the fixes that broke v6.
Thanks to all who helped create those instructions!
My question is - if I now update my ATV OS to v6, will I need to reinstall and reconfigure the certificates?
I would however suggest always backing up all the cert files, it means you do not have to generate them again and can add them to other machines/ATV's knowing they are all the same.