FPV antenna tracking is now working in HappyKillmore's GCS v1.1.32 and newer.
Are you looking for something to do with your original ArduPilot now that you've got the new ArduPilot Mega? Why not put it to good use! Diego Colonnello and I have come up with an antenna tracker for my GCS. It uses the original ArduPilot, a couple servos and a FTDI cable. Building the actual mechanism to move your patch antenna is up to you...but the code is in there to make it work. You can also use your ArduStation! Simply select the ArduStation output type and the data will flow out in the right format regardless of GPS or Auto-pilot brand.
Here's a Wiki page trying to explain how it works: http://code.google.com/p/happykillmore-gcs/wiki/Tracking
To download the ArduTracker 1.0 source and 1.1.32 of my GCS: http://code.google.com/p/happykillmore-gcs/downloads/list