Well I replaced the mode door actuator today... YAY it's fixed. No more clicking. I took a video and some pics for those that might have this problem.
I hope you enjoy working upside down and with your left hand if you have this problem. No cussing involved tho so it's really easy.
http://www.youtube.com/watch?v=bYhFpytR7fg
Here's a video of the problem.
Lower your Glove box and it's up under your dash.
See the red connector on the right... yeah thats the plug for it. The bottom left corner is part of the dash. This is taken from the passenger side looking toward the driver side and under the glove box.
Here's a better picture of how it sits under the dash.
Here's the old and new actuator side by side. Notice the position of the arm. The new one is on the right.
So I took it apart and found a broken gear tooth.
I've been reading on diferent forums and after searching for the part number that Ford did a craptastic job engineering this actuator. There is no physical limit switch for the door. It has an over current sensor that is tripped when the door is closed and jams shut and the motor can't turn anymore.
I really hope this will help anyone with the same problem but chose to ignore it because it's just an audiable pain in the butt for a second or two. If you ignore it, sooner or later you will only end up with either fully hot or fully cold and no in between.