There is only one heater hose attachment on a Ford water pump. It is the lower fitting. The upper fitting is a bypass hose and needs to connect to the small port on the stat housing. The secondheater hose connection is on the intake manifold right behind the thermostat.

Be sure the thermostat is facing the right direction. You can test its operation in some boiling water on the stove. Use a thermometer to see when it opens.