Okay. Water pump works fine. With the thermostat out, the car stays cold. With any kind of thermostat in, it boils over. Top hose is hot and bottom hose is cold. The water seems to not be flowing, but all passages are clear and open. New radiator, and when flushing engine, it flows right through. Am I missing something?

It seems strange to me that the bottom hose runs to the thermostat housing. Is this how it is supposed to be?

bottom hose cold? and your tstat is on the bottom hose? then you have a bad tstat. replace it again. the only way this wouldnt be the case is if your radiator or water pump was bad/clogged, or you have a completely blocked water passage in the engine.