The pin 13 direct from the Arduino is not capable of driving the DC-DC converter itself. You need a power mosfet, or some other form of transistor, to switch the power. The best solution is to feed your d.c. supply into the converter, then use the second circuit in reply #11 to switch your 2.5V or 3V supply to the pump. I can't see enough detail in your photos to know whether you have done this. Can you draw a clear schematic and post that?
You must connect 0V from the Arduino to to your proto-board! Have you done that?