1969 Ford Mustang engine popping

I have a 1969 boss 429 whose engine is not running so great. Starts fine. Problem is when you acclerate it wants to pop, surge, like it is just not running smoothly. WE have changed the plugs and wires, new points new condensor carb was rebuilt by pony carbs reset timming nothing seems to help. also water level in radiator is always low. It does not run hot (we put in an electric fan) but the water level stays below the core of the radiator. I am not sure if this is part of the problem. Anyway looking for help.
Bob