Yes, the throttle should still work correctly with the cruise control and brakes unplugged.
Having experienced what can happen when wires are shorted you might want to ensure that the 4 wires on the motor harness for reverse and pedelec, and the 4 wires on the control harness for the horn and headlamp, are all safely insulated from each other
(if they are not already fitted with connectors) to prevent any more unwanted short circuits.
I hope you get your wiring sorted soon.
Alan