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The clicking sound is coming from the actuator motor that controls the blend door. It's common for the connector to the plastic blend door to break, causing this symptom. This door regulates the amount of air that is diverted through the heater core and depending on how it breaks, it can also cause strange air flow problems.

This is a very common failure on this model and the fix from the dealer requires removing the plenum box and replacing the air flow components. This is a labor intensive process and expect to pay around a thousand dollars for the fix. There is an aftermarket kit that accomplishes the same fix and replaces the plastic components with a metal replacement. It won't break again and is much much less expensive than the Ford method.

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Q: Why is my Heater and defroster not blowing hot air and the heater making a clicking sound on a 1997 Ford Explorer?
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