Well, the colors on the wiring harness might match the original throttle wire colors, but there's no reason they would match any other throttle (there is no "standard").
Commonly, from the throttle, red is 5v, and black is ground, and whatever is left is the throttle out signal, but those are not universal.
Some throttles also have a voltmeter on them, which would take battery voltage, which also could be any color wire. I don't like using that because if water gets in there it can kill both the controller and the throttle by shorting battery voltage to throttle signal or 5v.
Since you have the controller opened up, you can do a continuity test from the exposed end wires to the pads inside the controller, and see which wire in the harness goes to 5v, and which goes to ground, and if there is one that goes to battery voltage. The last one should then be the throttle signal.
If the wiring is wrong, it's possible to damage the throttle, and the controller, especially if there is a battery voltage wire. Damaging the controller is much less likely if there is no battery voltage wire, but it has happened to people before.