My guess is it is your VRCM, try to hot wire the fan from the battery first off just to make sure it does still work,
1. if it still works i would suspect it is your VCRM
I had the same problem and didn't want to pay the 350 from ford so i just hooked mine up to a switch, however i really :q:q:q:qed myself doing that cause i had it on high all the time and burnt up many alternators before i realized that there was a low setting