Oh this is a very good point.
We forgot to add it clearly. You will be able to set the wifi the same way you would set the wifi on a normal arduino yun.
once you have reseted the arduino yun with the firmware from the sd card, you connect to the same arduino yun wifi network as before and you log in the same way as you would log in to reset the firmware.
But this time you change the wireless parameters. It looks something like this image here:
Then push restart and your arduino should be loged in via the new network parameters.