I replaced my fans just over a year ago after one of them decided to lock up. I bought a Dorman from what I can tell. Not sure as to why I did this, since everything I read.. is bad about the Dormans. lol 
Anyway, just over a year and my a/c starts blowing hot and car overheating. I am in florida so a/c and cooling are important. 
Behold the darn fans are not spinning. seems to time out after 10 or 20 min and not come back on. Went to autozoo and ordered a replacement module ($175), just to find out is completely different than the unit I installed in the car. :-( 
  
I am going to get a used fomoco unit on monday.  
If I can find my reciept for the dorman... I am contacting them.  
p.s. had no problems with it until now. 
  
AS far as the A/C.. the fans (no tow) or fan (tow/high ambient) should stay on and be Pulse width controlled by the PCM.  
  
Funny part about that diagram is that I dont remember there being a third wire for the PCM to the FCM. just power and ground. 
I would guess that the programming in the PCM is different for tow package, and possibly even the transmission. 
The Harnesses are different, and very expensive, about 6 versions (edge and mkx) that I can tell. 
I would like to see Ford answer this question we all seem to have.  
being in Florida, and towing a small boat once in awhile, I want to keep the rad cooler. 
  
Note: the module I got from Autozoo was a Duralast but the item in the box is labeled FoMoCo. :-)