Everything you did should help, but you might have a few little things working against you....
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It is a 17" 7 blade set just inside the fan shroud.
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The factory fan is about 19-1/4. Your fan is too small. The fan should be about 1/2" away from the inside rim of the fan shroud.
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Fan is about 1-1 1/2 inches inside the factory shroud.
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The fan should be about halfway in the shroud.
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The water pump has the steel impeller.
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People have had issues with the steel impeller and overheating. Not sure if the clearance trick is as effective with a steel impeller. You might try going to a factory cast iron impeller and set the clearance .030". If you need a factory pump, let me know.
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boil out into the overflow jug.
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Again see, if the cooling system will hold pressure. Boiling concerns me. The radiator pressure test kit from Harbor Freight is pretty cheap. Another way is after a drive, squeeze the upper radiator hose. You should feel that it is pressurized. How long does it stay that way?
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the nipple that screws into the heads that it came with.
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The Pontiac nipple had a flow restriction in it. I understand if you just put a plain nipple in there, it can cause issues, but not as serious as you describe.
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As far as drilling the block , I guess I'm not familiar with that process??
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Early 60's Pontiac engine blocks had two additional cooling holes near the center cylinders. Pontiac head gaskets still have these holes and can be used as a template for drilling them. Suppose to aid cooling of the center cylinders.