With all the hubbub lately regarding the different styles of water pumps and heater coolant flow, I decided to take an old water pump that I had and do a little research.
Here's what I've been able to confirm;
The heater port at the top of the water pump IS connected into the inlet side of the pump and as such would be the return for the heater. This is what I suspected, but I didn't want to stick my nose into that argument until I had proof.
Also, in regards to the by-pass setups. The pum