I suggest something like this:
Nov 04 Arrival Tokyo HND (Staying Tokyo Nov 4-13) (Pasmo IC Card
https://www.japan-guide.com/e/e2359_003.html)
Nov 05 Explore Tokyo (Pasmo IC Card)
Nov 06 Explore Tokyo (Pasmo IC Card)
Nov 07 Day trip to Yokohama (Pasmo IC Card)
Nov 08 Day trip to Kamakura (Enoshima Kamakura Free Pass
https://www.japan-guide.com/e/e2358_003.html)
Nov 09 Day trip to Hakone (Hakone Free Pass
https://www.japan-guide.com/e/e2358_008.html)
Nov 10 Explore Tokyo (Pasmo IC Card)
1JRP Nov 11 Day Trip to Nikko (JRP)
2JRP Nov 12 Explore Tokyo (Pasmo IC Card, JRP for JR lines)
3JRP Nov 13 Train Tokyo to Takayama. Afternoon Arrival. Check out Old Town Takayama. (Staying Takayama Nov 13-15) (JRP)
4JRP Nov 14 Takayama Morning Markets. Afternoon Day trip on Shirakawago. (I recommend this tour
http://tour.j-hoppers.com/shirakawago_tour.html)
5JRP Nov 15 Train Takayama to Osaka. Afternoon Arrival. (Staying Osaka Nov 15-23) (JRP, Pasmo IC Card)
6JRP Nov 16 Explore Osaka (Pasmo IC Card, JRP for JR lines)
7JRP Nov 17 Day trip to Hiroshima (JRP, Pasmo IC Card)
Nov 18 Explore Osaka (Pasmo IC Card)
Nov 19 Explore Osaka (Pasmo IC Card)
Nov 20 Day trip to Nara (Pasmo IC Card)
Nov 21 Day trip to Kyoto (Pasmo IC Card)
Nov 22 Explore Osaka (Pasmo IC Card)
Nov 23 Depart Osaka KIX (Pasmo IC Card or single tickets to KIX)
Activate Japan Rail Pass for Nov 11-Nov 17
Get Pasmo IC card at Haneda and preload as you need along the way. Good use for IC cards is also very good to use at vending machines and convince stores.
Kyoto, Nara, Yokohama and even Kamakura is pretty affordable train prices.
Hope this helps! Have fun!