Hi Andy,
Well, Rommie already has a server built to use the new master server (see
http://rommie.lithfaq.com ).
Registering the server however is only half the deal. In order to join the server, the client side cshell.dll and the one specified to the server (if no rez specified in customrez.txt, it's the regular 1.096 version chell.dll) must be the same. That basically means that a modded client to use the new master server can end up not being able to join the server, although it is listed.
Further more, since it doesn't use the new communication protocol, it will not be able to update the number of players joining or leaving, or when the map changes. And if there's no update for a server within an hour, it is then removed from the database.
Now, the best approach is to use either rommie's server (to still have the IP banning in) or have the guys that build your server contact me for an archive of needed files. I am considering a tutorial accompanying these files, but that won't come out sooner than the weekend.