I think it haves to be one of the stepper motors. One thing that saved me some time is focusing which side of the radio as for which stepper motor is causing the noise. Both sides are easy to access the stepper motors, but it saves time knowing which side to target. Have a look at this thread...
If anyone experiences an annoying click-clack noise under the passenger side dash, In my case, on all (3) of my 2003-2005 (should apply to 2000-2205), the noise was the air inlet motor (see diagram). In my case it did not require replacing the motor but to simply re-arc the motor position feedback wiper springs (see photo). When these loose tension, the motor will over-travel, causing the annoying click-Clack noise when set to vent (fresh air).
I've seen on this forum where the root cause was a physically damaged plastic gear but in my case there was not enough spring tension in the feedback wipers causing the HVAC controller to hunt for the correct position. All I had to do was increase the spring tension a little on the wiper arms. In my case, it was the stepper motor on the drivers side which is real easy to access.