Ditch the m-button. You'll have relentless issues using it in conjunction with an electronic ignition and those handlebar switches. I know it seems "easier" but honestly, it's much easier and more reliable without it.
Everything on that PDF is relevant to your install, except the Koso gauge wiring. Use AUX to provide "black light power" for your gauges. Also, run AUX to the Dyna.
To integrate your KILL switch:
AUX to Dyna on one branch
AUX to KILL on a separate branch
KILL/RUN to coils (stock BLK/WHT)
So you'll have 12v to coils when RUN is on and KILL interrupts the power to coils.