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The additional hole is for running an additional water line to the side of the cylinder head for racing. (Not needed on the street)
The stud and nut going to the two upper bolt holes are for belt tension adjustment if you use a single gilmer style belt from the crank to the water pump. Not needed if you are using a v-belt set-up. But they must be in place to keep water from leaking out of them.
I don't think you're talking about what I'm talking about.
I know what the two water intlets are for. One is for my heater, the other is to be plugged.
The "5th hole" I'm talking about is the one in the bottom middle of the pump that does not have any through-way to the coolant. It's just a threaded hole.