Mark may be better to answer you here but the wiring diagram will give you everything you need to know if you understand electonics. HOWEVER, even though the wiring diagram at the end of the manual shows the FULL wiring it is broken down to the various circuits a little earlier in the book.
I'm up to my butt in wiring on the custom bike we are building now and it's been challenging to say the least. I'm fitting a custom gauge set, custom hand controls, and additional sensors. I am making it all "plug and play" which is a little more work too.
Of course the wiring has to be reconfigured to even make some of it work correctly. For instance, the start button on the yamaha is a two position switch. When pushed in it turns off the headlight but turns the relay on for the starter. When out the relay is off but the headlight is back on. The start button for the controls is just for the relay. So, my options are to hardwire the light on or in this case add a switch to turn them on and off manually if so desired.
The turn signal was a bit more complicated since there are 5 wires on the Yamaha setup and 4 on the aftermarket hand controls. Not only that but the Yamaha button is a momentary button with the ability to shut them off by pushing in the button in the center position or leave it and the timer/trip meter will cancel it (self canceling feature). So with it wired up now the signals will only turn on/off by turning the buttons on/off. I could have used a momentary switch too but then the only off feature would be the self canceler. I elected to have them be the on/off which actually has the bonus feature of being a hazard lights if both are on.
There is more to what I am doing but it's not all fun and games. Harley hand controls, German custom gauge, and old style senders for volts and temp. I'm getting closer thankfully.