I posted this last night on yamahasupertenere.com but its easy to over look so I thought I'd post it here as well.
I learned today that there is no need to remove the seat and cut wires, or remove the tank and un-hook the fuel pump. The process Lobo described is basically correct. With the key off, press and hold both buttons at the same time.
While continuing to press both buttons, turn key on and keep holding the buttons for 8 seconds.
You will then see this:
Let go of the buttons, then press both again for 2 seconds.After 2 seconds you will then see:
From here you can scroll through the codes using either button. As Lobo said,to clear the codes,you then toggle the on/off switch. Then turn the key off and the codes will be clear. I hope this helps and makes it easier in the future.