Here are some things to check
No offense, but your son has obviously been mislead in troubleshooting this problem. And without a doubt so is the Ford Dealer. I mean what do they know about a Supercharged Cobra, I have found out from experience and lots of dollars that it isn't much.
What is happening is this. The Cobra doesn't have that much difference in the computer than any other 4.6L V-8. The cars computer is sensing that there is WAY more air being pushed into the air intake tube than normally required to operate the engine.
This "measure" of air is taken by the MASS AIR FLOW (MAF) Sensor, which adjusts things like injector opening frequency and ignition timing in order to comensate for more or less air passing through the sensor. And, if your a motorhead, you should know that if the timing is "bumped-up" too much that it will cause the temerature to rise drastically.
Now, by swapping the stock MAF Sensor for a more throaty (is that a word?) 70/75mm Mass Air Flow Sensor, the computer will sense a "READ NORMAL" amount of Air passing throught the meter and change the ignition timing accordingly, in turn, reducing your temp and saving the day. He will probablly pick up a few extra horses in the process. Also, change the thermostat to a lower temperature.
After owning two saleens ('89 and a '93) and three Supercharged cobras '95/'96/'93 (I still have the '93) I know for fact that these are top priorities to check, because if your car runs too hot and gets enough boost it will blow a head gasket faster than you can get a good jump off the starting line.
If ANY of this is news to you, and/or if it helps, please, e-mail me back at email@example.com. Then I will let you in a few secrets to REALLY give that COBRA some VENOM.