@iko - All the Rachio C terminals are actually connected together, so there aren’t any specifically for sensors. The Rachio M terminal is for either a Master valve or a Pump Start Relay. You may have a pump start relay to start the well pump, unless it has a pressure tank and starts when the pressure drops.
Do you have a before picture showing where those wires went in the Hunter system? No need to move over any power wires (24 VAC, ground or 120 VAC from the hunter system).
The very thin red and black wires in their own grey jacket may go to a rain sensor.