How can i trigger this watering timer manually
The 2200uF capacitor is rated at 25V, and appears to be connected through a diode to an inductor which goes to battery positive and a transistor which switches to Ground. This looks like a voltage booster circuit. It probably just charges the capacitor to a high voltage (&lt;25V), which is then discharged through the valve 'motor'. This may explain why no DC voltage is seen when the valve is operated.   

The third photo appears to show a transistor H-bridge controlling the valve with blue and black wires. One side of the H-bridge appears to be shared by both valves. 



I suspect the valves are magnetic latching solenoids, and the coils wound around the outside are for the controller to tell when they have operated. A latching solenoid is operated and released by sending a pulse in one direction or the other. You could do this 'manually', by breaking the connections between the control chip and H-bridge inputs, and feeding in digital signals from your own MCU. 

The voltage booster may be driven by the control chip and is probably only turned on when needed (ie. a few seconds before operating a valve, and only until the capacitor has charged up), so you might need to provide your own drive for this also. Alternatively you could try charging the capacitor up from an external high voltage source, with a resistor in series to limit current when the valve is operated.     

Before doing any hacking you should trace out the circuit and make sure you understand how it works. H-bridges tend to blow up if given the wrong inputs!