That is too bad cleaning did not take care of it.
I am not sure if I understood the two questions, but will try. Each valve uses two wires, “common” and “hot” (24 VAC). Both are needed to open the valve. Are you positive the zone has three sprinkler heads and only one is operational? Could there be a manual valve or something between the operational head and the two non-operational. Concerning the wire into zone 12, do you know where your valves are to be able to count? Do you know if you had 12 operating zones with the Rain Bird?