An FMIC seems like a drastic solution. Hmmm, I've got a zit. I NEED A FACELIFT!!!
We are running a stock JDM alt with the GM e-fan Cake recommended in his e-fan how-to controlled with a push-thru thermoswitch pulling air thru a Godspeed rad. It was 104 in the shade last week and I drove the car in traffic to the office with the a/c on and the Pioneer 7" LCD head unit on and had no issues with heat or voltage.
I would start by seeing if I could get my hands on a stock alt or at a minimum having yours tested. If something changed after your short, that would be the logical place to look.
Alternatively, Id swap to the GM fan. Maybe it doesnt have the watt-consuming machismo impact of the Ford fan, but yall don't spend much time above 104 there so it'll probably keep temps managed.