2003 Chevy Impala Overheating

Engine Cooling problem
2003 Chevy Impala 6 cyl Two Wheel Drive Automatic

I noticed the temp gauge showing hot checked the radiator and there was dark brown mud under the cap and was low of coolant. I cleaned the gunk out of the top and top it off. Problem persisted until the water pump went out, replaced water pump, disconnected hoses and ran water through the radiator until it was clear(i realize this is not the proper way to flush the radiator)also ran water through the motor---prob persist brown mud and overheating. Replace radiator and thermostat and used (i believe it was) johnsen radiator flush, cleaned out overflow bottle. Still overheating but no more mud. Heater not blowing hot air.