What kind of sensor are you using? From the looks of it, you were running the system in bypass mode, meaning that at least rain sensor was not being used. I believe that other types of sensors available to Hunter from products like solar sync are not compatible with Rachio. This should not be a big loss since Rachio is designed to gather that data over the internet connection so you could stop using the sensor all together without major drawbacks.
As far as the valve, I'm assuming you are asking about the master valve, not one of the zone valves. Your master valve appears to be connected to the bottom zone terminal via a thin red wire. The terminal is labeled "P/MV" on your controller. You will need to connect it to the M terminal of the Rachio, it is on the middle top terminal block next to the sensors.