To help you sort things out, here's the factory Custom Cruise III wiring diagram for reference to the cruise control wire colors and routing...
The cruise control wiring is
independent of the stop lamp wiring.
The stop lamp switch (not pictured in the diagram above) has only two connecting wires: orange and white. Orange is fused B+ supplying power to the brake switch. White carries stop lamp power from the brake switch to the turn signal switch. Power divides through the turn signal switch then runs to the rear lamps via yellow (left turn/stop) and green (right turn/stop). Assuming that I understand your question and you are completely eliminating the cruise control, you should be concerned only with the white and orange wires that terminate in a two-terminal plug.