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The four pin ballast is for electronic ignition. Your new wiring harness probably has an ECU connector as well. I would get the right harness unless you want to convert to electronic.
If you have electronic ignition already, with a four pin ECU then a two pin ballast will work. The other two wires in the ballast connector do nothing with a four pin ECU.
There are two ways to go. You could just connect the two correct wires to your ballast and call it done. Or you could install a dual ballast , and plug in the connectors the way they are. It might look cleaner. That way you could also run a 5 pin ECU. If your ECU quit in the middle of nowhere and the only one you could find was an old 5 pin, then it would work.