I now own this car, and this is still something to iron out. I did notice that when the car is running at temperature, the output from the heater is nowhere near what I would expect.
My question is why would a heater core cause overheating problems? A quick look at the setup, I followed the routing of the hoses to the heater core, and didn't notice any control valve/bypass valve. I have been away from Mustangs too long, but I thought there was normally something to control the flow of coolant to the core?
At any rate, the car runs cool at speed, and gets a little hotter in stop and go traffic (in 60 degree weather). Spyke recommended a small manually-switched electric fan, but I may go with full electric fan & controls and remove the flex fan.