Our 2001 Adventurer on the F53 chassis came with a 6 pin trailer connector and it works with electric brakes. When it came from the factory only 5 of the 6 terminals in the socket had wires running to them. The one not attached was for the electric brakes.
The wire was supplied by Ford but was folded back in the harness about 3' - 4' from the rear of the coach. I called Winnebago and was told that the only time it is connected is by the dealer when a customer orders an electric trailer brake.
When opening the flap on the socket on the back of the coach the wires in ours are as follows:
12:00 - Lights
2:00 - Tailer Brakes
4:00 - Left Directional & Brake light
8:00 - Right Dierctional & Brake Light
10:00 - Ground
Center- 12 volt hot (can be used to power internal trailer lights)
Our Expedition has a 7 pin connector and the 7th pin is used for charging a battery in a trailer. Even though I ordered the truck with the towing package I had to have the dealer plug the relay into the box on the left inner fender to get it to work.
Here's a link to eTrailer.com:
http://www.etrailer.com/faq/wiring.asp
They explain the basic wiring for 4, 5, 6, and 7 pin connectors. They also have a disclaimer that says all trailer wiring is not "standard".
Hope this helps.