This probably happens after you first start the car or change modes on the air conditioning system . It sounds like a mode actuator for the recirculation door or mode door or the temp blend door ! Some of these are hard to get to but drop or take out the glove box and turn the key on to isolate the one that is clicking ! Mode actuators are a common problem on fords for this exact concern !
Do you have a picture or diagram of rhe parts/ location
Sorry no i dont ! The actuators are square with a small connector - normaly there is one far right behind glove box its for the recirculation door . A little to the left there is another it will be on top of the hvac box or on the bottom this would be the blend door actuator . There is yet another alittle further left either on the front behind the radio or controls or to the left side ; this would be the mode actuator ! If it makes noise when you turn the key on you should be able to see each one of them ! You can get diagrams from the ford dealer or mitchel repair manuals ?
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Air/Blend Door Actuator Modual is defective: See info below
Description :
Temperature Actuator
Attributes :
Controls the blend of hot & cold air
Make :
Ford
Brand :
Dorman - OE Solutions
Application Notes:
Please select Detailed Applications
for Application Note information. 
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