Ian,
surprised to hear you had to still raise the nose of the car. Once the coolant pump is primed through the expansion tank shunt hose, it should purge the air through the heater/bypass circuit as soon as you start the engine. The problem with the standard setup is that the pump remains airlocked and cannot generate any head of coolant pressure. Once airlocks in the bypass and radiator circuits are purged, the air should find its way to the header tank so you may need to top up to achieve the correct coolant level.
John,
I suspect that keeping the header tank shunt hose anywhere on the original bottom hose (including the standard submarine position) will be a bit prone to airlocking during filling, even if you have removed the standard thermostat to fit the PRRT. This is due to the rather tortuous route it takes, and especially if it is a dry sump type bottom hose.