Flickering or pulstating Headlights

The car has the relay installed and runs fine, except for the pulsating voltage. I have the old style regulator installed and the relay is installed per that diagram. Where I am confused is I now have five wires where there were four in the connector that replaced the ballast resistor. Should one the original wires be capped? Thanks again!

If the original wires are not being used then yes they should be capped or better yet snipped off and tapped. As long as your car is running fine and the alternator is charging then you should be fine. Sometime in the future (if you are running a isolated field alternator) you might want to consider switching to an electronic regulator as it will help give you a more stable voltage.