only a couple other things ive seen from reading this that havent been checked and can do everything you said, the radiator cap and the heater core. if your rad cap doesnt hold pressure your boiling point will be fucked and the car will overheat. if the heater core is plugged up the same thing will happen. also get the cars cooling system pressure tested somewhere, it may have a warped head or a blown gasket which would also cause your problem.
also if you wanna see if the water pump is working expose it and stick a long pipe up to it and listen, if its sounds like its swishing away then it is.