Voltage Regulator problem

Okay I got the harness all unwrapped. There are only 2 wires coming out of the alt. 1 larger gauge wire which I assume is the charge wire? It goes into the bulkhead connector.
The other smaller wire goes into this junction which has been laying on the intake manifold since I got the car
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then it T's before entering the bulkhead.
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From the T 1 wire continues onto the ballast resistor
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and the other just dead ends at this connector near the battery
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