Cannot find the common wire in "box #2" on a three way circuit
You may be confused as to how 3-way circuits work, since you seem to be expecting certain colors, and are discussing "on" and "off".   3-ways do not have "on" or "off", they merely have "traveler 1" or "traveler 2". 



The two travelers are interchangeable, and always run together in the same cable (with a third wire to complete the circuit).   They are almost never yellow, but I recommend you mark them with yellow tape on both ends - it makes it a lot easier to understand and work in 3-way boxes.  

They can be any combination of the wire colors in cable - red/white, black/red, or black/white. This can even change in the same circuit!   That's why I recommend re-marking them.  

I am fond of picking the traveler colors so that the remaining wire is the color of its function: white if neutral (in fact this is mandatory), black if always-hot, and red if switched-hot.  

Once you are clear which wires are the travelers, make sure the travelers are landing on the brass screws on the 3-way switch.  The black screw goes to the always-hot or switched-hot.