The way James redid the cooling system eliminates the thermostat on the lower rad hose and also removes the bypass line(you know the line that runs from the coolant cross over tube down to the thermostat housing to allow coolant to circulate through the motor until it reaches temperature and opens the t-stat to allow flow into the radiator)
The system stock will have coolant try to flow through the radiator while the engine is warming up and then it will dead head on the bottom radiator hose when it reaches the t-stat which is closed. So that is why there is a bypass line from the coolant cross over tube down to the factory thermostat housing so flow can come out the heads and enter back into the lower rad hose to feed the water pump again.
Big problem with our stock cooling system is the factory oil cooler setup is a very small ID and restricts flow back into the block. Evans designed a system similar, but there setup didn't remove the bypass line and I much prefer the t-stat housing James and Ed found.
Does that help Josh?