This sounds like air lock to me. Did you bleed your coolant system at all, or just re-fill it? Do you know the thermostat opening temprature, sure you got the right one?
First thing to try is bleeding your cooling system, this must be done with the heat on full hot. Put a bleeder / or some kind of funnel rig into the top of your rad, and let the car warm up. Keep topping up the coolant, and check for bubbles. There is another bleeding screw in the manifold I have heard of, but I'm not good with RB25 motors.
The waterpump is not the issue- because you would not have got 40 mins of driving with a broken pump without overheating.
Other option is simply its too cold out in your winter, and the heatercore is cooling the motor enough not to need the flow of the radiator.