The only thing I can think of that actually has moving parts is the water pump so that's really all it could be IMO and the truck does have a new pump and TB on it. It's shiny and pretty.
So remove three bolts and flood the engine like a river with a hose. Are the coolant lines a straight shot through? It has to stop at the thermostat somewhere, which case it won't clean on the other side of it.
Maybe do the cleaning, do 100% water and just get the engine warm enough to open the thermostat, shut it off and let it cool then re-flood everything?