All I can tell you is on a blown 4.6 Cobra, Northstars, Ford Big Blocks, Honda Civics, Ford 3.0 Ranger and a 3.4 Toyota is that they all were overheating without a thermostat and ran proper with one.
As DLF said, the water needs time to properly cool in the radiator andthen refill the block so the water that was in the block can now cool in the radiator. Thermostats dont just open and then stay open, they cycle like most controll valves do in the car.
Now Mlschultz car is not one I could say without playing with. Different fans, dfferent rad and an intercooler are not what Ford had in mind when they designed that cars cooling system.
That being said, Mlschultz, you ever think of running a cooling line from the rear of the drivers head to the passenger head? I did it on an 03 Cobra and the car always ran 12* cooler after that.