If you are saying that the distance from the back side of the radiator to the shroud surface is 3/4", then your thoughts about that being too small are correct. Going down the road, the air is probably piling up and the only air flow is essentially the diameter of the fan hole. The flaps you refer to are usually a rubber flap that are simply pop riveted to the fan shroud and covering holes cut in the shroud. You might call some pro like Griffin Radiator and ask how much space they recommend between the radiator core and the shroud.

Another thought is perhaps your fan is helping to limit the flow at highway speeds. Can you switch your fan off on the road to test?

mike in tucson