Josh:
ECU wiring:
4 pins on the box 5 wires...yes it is ok like that...(newer system)
Alternator connection:
You should have three wires attached to your alternator. The large gauge wire under the screw terminal goes to the battery. The other two should have spade connectors to the field windings in the alternator.
One of these two should be connected to switched 12 volts (12 volts ONLY when the key is on). On the diagram below this wire is blue with white tracer. The green wire goes to the voltage regulator.
Hope this helps.
Please notice....BOTH field wires run to the voltage regulator, the switched wire (blue) is just T'd off instead of going straight to the regulator(it makes several other T's as well). That diagram is nearly identical to my '87 for the charging system, minus the ballast resistor.