Well, in that case my first thought is that you've got an air bubble or two in your system. The Cobra owners manual gives a specific order of operations for filling the coolant system in order to avoid bubbles. When the car is cold, you should make sure that the overflow tank cap is off and then remove the fill plug from the crossover tube. If the tube is dry, add water until you see the level come up (the level in the overflow bottle should be at the same height.
Start the car and let it idle with the fill plug installed but with the overflow bottle cap off. If there is an air bubble in the system, it should eventually vent to the overflow bottle, and you will notice a drop in level. Top off the bottle to the FULL line and you should be fully burped. If you are confident that there are no air pockets in the cooling system and the car is still overheating, I would look into whether that 1996 radiator is sufficient. Most 96 cars were given a 97 spec radiator during the TSB, but there might be a few cars out there that didn't get the update.
BTW- the 4.6 DOHC cooling system is a much different flowpath that what you would see on the earlier cars and 2V cars. It looks weird, but it does work.