My guess is at the HVAC unit too. I'd check all the pins on the connector and then look at the back to make sure the wires weren't pulled out of it at all when switching head units. If those are all fine, you could check further downstream to see if the wires have been pinched or frayed at any point.

​​​​​​Electrical problems are always tricky, but it sounds like you have a good handle on this. I'll be following this thread to find out what the true cause is!

 

Did you ever figure this problem out?

 

fan clutch replaced, sadly no difference - will just have to live with the crappy loud fan...
Some people have swapped to an elec fan, something i won't do.