I think I may have found the source of my problem.
When going through each of the hoses to check for sediment etc I removed the expansion tank to flush it out too. Once removed I heard a rattle from inside. It was a pebble!!!!!
So I think it had been blocking the return side of the cooling circuit when it sat covering the outlet. Hot water from the thermostat housing overflow would have been coming in at a quicker rate than the return side, filling up the tank to overflowing.
I need to get a new water pump gasket and rebuild everything tomorrow to check my theory.