Several folks have used one of these screw shields with a Mega to connect up lots of wires for model railroad setups. 54 IO connections. Do you need to control higher voltages or currents? Adding other components may be needed. http://www.crossroadsfencing.com/BobuinoRev17/
What output do you want? 5V? You need a boost regulator circuit that will take battery output and boost it to desired level for as long as battery can supply current. Example: http://www.pololu.com/catalog/product/798
Please turn off your Caps Lock, that's like shouting. Have you loaded any sketch into the Nano? If not, the blinking is likely just the bootloader letting you know the board is alive. (white light? didn't know arduinos used white lights)
besides the comparison vs assignment mistake (happens to all of us, gets better with practice ) check the forward voltage drops of the colors. Not quite sure what you mean "These pairs are wired in series for reference." but Green/Blue usually have a higher Vf then Red, like 3.2V vs 2.2, so that might keep them from lighting up also.