Do all this with the ignition off and battery disconnected.
Remove the left hand Side cover and locate the starter cut out relay (the biggest connector) There should be a black wire in the connector block, this is the most likely wire you connect the wire that goes to earth when you press the starter button to. Using the meter buzzer (does the meter have a buzzer?) to trace that wire to one of your black wires at the duo connection point and connect it to the starter button earth wire. That is the easy one and you should now have a working starter motor.
If the installer used the Yamaha alarm connectors then it should be relatively easy to find which is which, but since that is unknown it will require a little more work and it will mean disconnecting the plugs on the ECU to try and find it.
With the wire that goes to earth (ground) when you switch the ignition on, does it go off if you put down the side stand or put the bike in gear?
Remove the left hand Side cover and locate the starter cut out relay (the biggest connector) There should be a black wire in the connector block, this is the most likely wire you connect the wire that goes to earth when you press the starter button to. Using the meter buzzer (does the meter have a buzzer?) to trace that wire to one of your black wires at the duo connection point and connect it to the starter button earth wire. That is the easy one and you should now have a working starter motor.
If the installer used the Yamaha alarm connectors then it should be relatively easy to find which is which, but since that is unknown it will require a little more work and it will mean disconnecting the plugs on the ECU to try and find it.
With the wire that goes to earth (ground) when you switch the ignition on, does it go off if you put down the side stand or put the bike in gear?