I sure hope that you did not replace a head gasket in an attempt to get your heater working properly. You had other problems with the head gasket, right? Because if someone sold you a new head gasket for a heater problem, they ripped you off.
If you have heat from your upper ducts in the dash but not the lower ducts, the problem is with the control door actuators inside the dash or with the climate control unit where the buttons are. It is not under the hood. Do you get no air at all flowing from the lower ducts?