The old control box has no function when an alternator is installed. The alternator has internal electronics that handle that function. The instructions I posted a link to appear to be different from the ones you used.
Succinctly, when an alternator replaces an generator, the wires on the generator control box are removed. The "large" wires are joined to each other and the small wires (EXCLUDING the black ground wires) are joined together. At the alternator, the old, large generator wire is connected to one of the large terminals on the alternator. The generator's small field wire is then connected to the alternator's small terminal for the charge warning light. Some take an additional step and run an additional heavy gauge wire from the alternator's remaining "large" terminal to the battery (+) terminal or the "hot" terminal on the starter solenoid.
Gutting a control box to achieve the alternator conversion is nice because you do not have to modify the wiring harness.