I have never heard of the engine ports getting stopped up, but I suppose it is possible if one fills the radiator with muddy water like the Japanese rice farmers do. Nothing saying that the new thermostat is not faulty. I would follow Eddie's advice and remove it for testing. You should be able to see the water flowing into the radiator by viewing from the removed cap. If it is flowing thru which it should be as all is new, then I would suspect a faulty gauge if the thermostat is working properly.
There is nothing else left that would make it run hot with all new cooling system.