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

That "junction" is a choke timer. it should be bolted to the intake....usually under a coil bracket bolt. The timer is part of the heat assist for the electric choke. Oh, and don't forget to tighten that exhaust header nut!