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In my 2003, I was able to minimize the clicking (thumping) in the rear unit by adjusting the temp to a sweet spot.I traced my clicking down to the LH temperature blend door actuator. This is, unfortunately, the one that can only be removed by either: (a) removing practically the entire front interior of the vehicle, which is listed as a 6+ hour job or (b) removing the shifter, center console, some ventilation, etc., which is about a 3h job. I'm not sure how I am going to approach this one yet. I don't have the time nor the patience to do that job myself, but I don't really want to pay someone $600+ labor to do it either. The person(s) that designed the system this way should be shot.
In my 2003, I was able to minimize the clicking (thumping) in the rear unit by adjusting the temp to a sweet spot.