A few impressions.....
Nov 1st is going to be painful - it is about 4½ hours to get to Takayama from Tokyo. And by that time of year it will be getting dark a lot earlier. There won't be a lot of time for the city. The Old Streets are crammed with day tripping tourists, so it is not as enjoyable as it once was. From evening the whole area is a giant ghost town. The only place open with the lights on over several streets was a convenience store. Kamikochi to me is biting off too much to swallow. It's just too time consuming as a day trip, and buses are not that frequent. Shirakawago is far more practical - and there is Gokayama if you want to avoid the mobs.
I'd also suggest seeing Osaka on Nov 4 or 5 after a day of sightseeing in Kyoto. The city is best in the evening - Dotonbori, Shinsekai, Abeno Harukas, Umeda Sky Bldg etc.
https://goo.gl/XE5R94For Nov 7, use the full day for Himeji: the castle, the Kokoen Garden, and Mt Shosha can fill up the whole day.
For Koyasan, get the Koysan World Heritage Tkt.
https://www.japan-guide.com/e/e2358_012.htmlAnd if you want to go to the cemetery at night, be sure to pick one of the temples that
does not have a curfewhttps://awesome-tours.jp/en/tour/night-tour-return-bus/There are tour companies that have paid tours but you can just go by yourself.
For Hiroshima City there is more than just the Peace Park - the Shukkeien Garden is wonderful. There is also the castle, but if short on time, then skip it. The Mitakidera Temple is also stunning and still unknown to the tourist hordes, at least currently.
Nov 9 - There is enough time, if you get up early. Don't miss the shrine, Daishoin Temple, and Mt Misen. If you are overnighting, look at this tidal info and see the shrine both at high & low tides. At low tide you can walk up to the giant torii gate.
http://www.tides4fishing.com/jp/hiroshima/itsukushimaJust remember that it will take about 5½ hours to get from Miyajimaguchi to Tokyo - you might arrive at night, but that is fine.