I just finished polishing Ardupilot_25.zip. The Manual will be finished this week.
I'm sure there will be a few setups that have issues, so be sure to check out the test suite which isolates each sub-system for testing. If you have any issues use this blog to post them. What's most important is that you include a log file of your issue enclosed with your comment, as well as a copy of your header file and notes about your radio and receiver.
By default the control switches are not set to Autopilot. This was intentional. I don't want people to start flying it right away without fully ground testing their setup. My suggestion is to get Stabilization working first, then move up to Fly-By-Wire. Once you can fly the plane in FBW mode, then try Autopilot.
I've also updated the GPS debug mode which is now simply GPS_PROTOCOL 5 (instructions are in the header file). Everything about the plane will behave normally, except Autopilot mode will cause the plane to think it's flying your waypoints. Ardupilot will output telemetry and indicate when it thinks it has reached each WP. You can control the speed of the simulation with the throttle control.