Here my thoughts on your trip. I would say overall quite okay, with a few possible tweeks:
26/10/17 Tokyo: Arrival at Tokyo in the afternoon. 27/10/17 Explore Tokyo 28/10/17 Explore Tokyo 29/10/17 Explore Tokyo 30/10/17 Day trip to Kamakura - Back to Tokyo 31/10/17 Day trip to Yokohama - Back in Tokyo
I would distribute the day trips more evenly across your days in Tokyo, but also make it depend on the weather.
06/11/17 Visit the Monkey Park and kurobe Gorge, continue our way to Kanazawa and sleep there (alternative stay again to Nagoya)
Monkey park and Kurobe Gorge and on to Kanazawa all in one day seems to be too much. For Kurobe Gorge, please check if it is possible to get the train tickets reserved, as I would think early Nov is high season for momiji. In the monkey park there will be no snow at that time of the year, so it is kind of less impressive, but I guess the place is still nice with the mountains an everything.
11/11/17 Visit Himeji Castle and may Mount Shosha and then continue our trip to Hiroshima and after our visit to Hiroshima, pass to Miyajima where we will sleep.
Agree with @firas, that you will not have time to visit Hiroshima on that day. It depends on your interests if you want to skip Hiroshima entirely or not.
14/11/17 Day trip to Takachiho and back to Fukuoka or maybe to Kurokawa onsen and sleep there. (Could it be possible to visit Takachiho in that time?)
Are you renting a car? I have not been to Takachiho, but to Kurokawa onsen, driving there from Matsumoto. I would say Takachiho and also Kurokawa-onsen are not day trips from Fukuoka, but places where to stay. And I think they are exclusive of each other. I.e. either one or the other. Not both on the same day. Note that the main street from Matsumoto to Asu is still closed as the bridge collapsed in the earthquake last year, so you need to take smaller streets. I definitely liked Kurokawa-onsen, and stayed there two nights, spending one day hoping from onsen to onsen. Very nice experience. I also still have Takachiho on my list of "to dos"
18/11/17 Kyoto 19/11/17 Kyoto 20/11/17 Kyoto 21/11/17 Day trip to Nara - Back to Kyoto 22/11/17 Day trip to Mount Koya and overnight there 23/11/17 Day trip to Sakurai or Ise? 24/11/17 We are still staying in Kyoto because we have booked from 18/11 to 25/11 (we booked it long account. It is a cheap room so we don't care to sleep elsewhere and leave our luggage there). Is it worth it to spend another day in Kyoto or to do a day trip?
Well, you can do Osaka in a day trip from Kyoto. (If there is something interesting in Osaka...). Again I would space out the day trips over the time in Kyoto. For Mount Koya, you need a night, so it's not a day trip. So possibly as you don't know yet what to do from 25 - 26/Nov, you could do the Koya trip on those days? For me personally there can never be enough time in Kyoto and Nara.
25/11/17 We still don't know 26/11/17 We still don't know
Possibilities include: - Koya-san (see above) - Izu peninsula (best with a car from Atami or an other train station) - if you wanted to lighten up some of your earlier travel days, you could do Magome & Tsumago on the return to Tokyo freeing up a bit of time in the earlier days of your travel to allow you time in Hiroshima. Also Shikoku is really overlooked. You will not have time in your itinerary for Shikoku, but if you manage an extra day or two between Himeiji and Hiroshima, you could visit Naoshima or Teshima, both very nice small islands, with very interesting art.
We know that in 32 days we may be able to visit some places in the north but there are so many things to see in Japan that we think we should sacrifice something.
Both the North and Shikoku are often overlooked, but it is your decision and you have definitely included a good number of highlights. Travelling in November, I personally would also shun away from the North, but I have to admit that I know little about Tohoku at all.
Due to our long stay, is it worth it to Buy the 21 days Japan rail + a 7 days Japan rail? Or Just a 21 days and then with individual tickets or Bus pass?
I have no idea about JR rail passes. But in general they pay off if you do a lot of travelling around, so for the days you are at Kyoto / Tokyo only the pass wont pay off, so maybe a 21 day pass might be sufficient. I also read that there is some Kansai pass, but I don't know if it is worthwhile for trip there.
Enjoy your trip to Japan!
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