Would it be possible to run the rain and flow sensors on the same wire then in firmware count puleses while a program is running and look for a constant high for rain while no program is running. A diode on the sensor wires should take care of backfeeding either sensor, and we would get the benefit of both sensors without the need for messing with the board directly.
This would also allow an alarm condition for leaks, or open valves while a program is not running because a pulse detected outside prescribed times would indicate unplanned watering. It would also allow for stopping a program if the ‘pulse’ goes solid indicating way too much flow or rain.