You stated that it has a new water pump, is it a Genuine RB25 std pump? As the VL and N1 pumps fit, but have less fins, thus don't flow as much water at idle, causing the engine to overheat.
Could also be a airflow problem. May be worth lifting the rear of the bonnet (near the windscreen), using washers, to allow better ventilation in the engine bay.
Also, if the front bar is more restrictive than a Skyline you will need a larger radiator than a std Skyline. I may be wrong, but i think the R32 radiator is smaller than the R33, so you may already caused a heating problem anyway.
Just another suggestions.
Alan