Assuming you are using the factory yellow top coil, it is designed for full battery voltage only when cranking the starter. So you are correct that full battery voltage when running is too much and it will overheat. The factory yellow top coil needs to be fed by the factory pink resistor wire (assuming it is intact), or through a ballast resistor if tied direct to battery voltage. Or you can replace the coil with one designed to be powered directly from battery voltage. Lots of discussion on the different options with Pertronix ignition here:
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