Wire your MSD TL as follows...
Purple wire into MSD controller box is a switched 12v feed in (use a waterproof switch or a waterproof plug-in connector)
You can pick up 12v feed from the battery lug side of the starter relay.
Four wires from a Yamaha OEM start/stop switch are red and brown for the relay feed and a black and white for the ignition kill.
Pick up a 12v lead feed from your battery lug terminal off of starter relay and connect to red to the switch (power source for start relay)
Connect brown from switch to relay (start feed 12V) the other feed terminal on the relay goes to ground (neg on engine or back to battery or a ground lug (is what we use))
White from switch to pink from MSD controller box.
Black from switch to ground or (see above)
Now the start, stop and tether switch will work as normal except you have to use the stop button like a dirt bike, you must hold down until engine stops turning over or get the above post relay wired in and then it will be just like a stock Yamaha.
Follow the rest of the MSD instructions for connecting the pickups and coils.
Chuck