Here's my suggestion - Reduce your Tokyo stay by one night (9/8 to 9/12). Make a two-day onsen trip after Tokyo - to some rural destination in the mountains (or Hiroshima if that's what you want to see). Then stay in Kyoto until the final day of your trip (9/14 to 9/20). Take the Shinkansen from Kyoto around 11am to connect to Air Canada flight 4 (Departs Tokyo at 5:30pm)

Or ... if you want to do a Hiroshima trip at the very end of your stay ... Take the train to Miyajima on 9/19. Stay overnight at Iwaso onsen. Visit Hiroshima in the morning of 9/20. See the peace park and museum. Take the bus to Hiroshima airport. Catch ANA3114 to NRT (Departs at 2:25PM). Connect to your flight home.