Help me make my itinerary work

I'm going for 3 weeks starting the last week in October. I'm trying to add an overnight in Nikko and an overnight in either Okuhida Onsen near Takayama or Kinosaki Onsen near Kyoto. My main concern is clustering too many train rides and single overnight stays together, but can't seem to figure out a good way to spread these out and make it flow better. I have a total of 22 nights and can change the sequence or the number of nights at a location if it's better.

Any thoughts or ideas would be appreciated.

Idea #1:

Tokyo 2 nights
Nikko 1 or 2 nights
Kanazawa 3 nights
Kyoto 6 nights
Kinosaki Onsen 1 or 2 nights
Osaka 1 night
Mount Koya 1 night
Hiroshima/Miyajima 2 nights
Tokyo 4 nights

Idea #2:
Tokyo 2 nights
Nikko 1 night
Kanazawa 3 nights
Okuhida Onsen 1 night
Takayama 1 night
Osaka 1 night
Mount Koya 1 night
Hiroshima/Miyajima 2 nights
Kyoto 6 nights
Tokyo 4 nights

Kinosaki only need an overnighter, and Kanazawa only needs a full day. So you can drop some time there and add it to other places like Tokyo etc.

Thank you Hakata. Any suggestions on other places to visit if I drop those nights?

How about this

Tokyo 2 nights
Nikko 1 night
Kanazawa 3 nights
Kyoto 6 nights (Day trips to Nara & Osaka)
Kinosaki Onsen 1 night
Hiroshima 4 nights
Mount Koya 1 night
Tokyo 4 nights

Personally though I would probably do something like this

Tokyo 3 nights (day trip to Nikko or 2 nights with an overnight in Nikko)
Kanazawa 2 nights
Kyoto 6 nights (Nara, Osaka, Hikone)
Kinosaki Onsen 1 night
Hiroshima 4 nights (Kure, Iwakuni, Takehara)
Okayama 3 nights (Naoshima, hike up to Bitchu Takamatsu castle, Himeji castle)
Tokyo 3 nights

What I have found, from an expense standpoint, is that Kyoto had more attractions that are on bus route. If you can get from Tokyo to Kyoto by a single discount ticket, or, by bus, you could probably drop from a 14 day JR Pass to a 7 day pass, and save money.

Since you might go to Takayama, go there by bus, and then take a bus to Kytoto. Here is the Nohi bus line web page:
https://www.nouhibus.co.jp/english/

The Nohi offers many packaged tours. Check out the Spa and Shinhotaka Rpoeway ticket:
https://www.nouhibus.co.jp/hida/bustrip/?lang=en

Note: I have not gone to Kanazawa yet, I will locate that at the end.

When you are done in Takayama, you would head by bus to Kyoto, and probably also visit Osaka and Mount Koya. This would involve a few train rides, and getting to Mount Koya also does not use a JR Pass. The rail is owned by a private rail (Nankai Line), and so the JR Pass still would have little benefit.

After Mount Koya, visit Hiroshima, Miyajima, Kinosaki Onsen, Kanazawa, and then go back to Tokyo. This could all be done with a 7 day JR Pass.

I would look into one of the Tobu Nikko passes to go to Nikko.
http://www.japan-guide.com/e/e2358_002.html
If you do plan to spend two night at Mount Koya, think about getting a 3 day Kansai Thru pass, and use it to travel from Kyoto to Mount Koya, and then back down to Osaka. You could also use the Koyasan World Heritage Ticket, but it is a two day pass, and would only works for a one night stay.
http://www.japan-guide.com/e/e2357_005.html
http://www.japan-guide.com/e/e2358_012.html

I hope this links help you to plan your trip. Good Luck!

Stan - your suggestions are very intriguing. Would you mind saying a little more about your reasons for your itinerary choice?

I considered Shikoku, Matsuyama, Naoshima but ended up deciding that there was so much to see in that area that maybe I should leave it for a future trip.

Because I will be in Japan the last week in October and first two weeks in November I was thinking the Japanese Alps might be a good area to see some beautiful fall color.

Your suggestion for Okayama and more time in Hiroshima is appealing to me. One concern I have had while planning is the fact that almost everywhere we are considering is heavily on the tourist trail and I assume will be very crowded.

ebayChucky - thank you very much for all the detailed travel information. You helped me to realize that I shouldn't just buy JRP without considering other options.

In terms of fall colors, the time of year that you are traveling is a little early for Tokyo, Kyoto, and Hiroshima. You will have to go to higher elevations. You have already put Nikko and Mount Koya on your plan, which are good higher elevation choices. The alpine route, as well as the Kurobe Gourge (from Kanazawa) is also a good choice.

Last year, Nikko was at peak colors on the 10/18 report:
http://www.japan-guide.com/blog/koyo16/161018_nikko.html
Putting Nikko at the start of your trip is very good.

The 11/01 report of Mount Koya show the start of the season:
http://www.japan-guide.com/blog/koyo16/161101_koyasan.html
Placing the visit when I suggested also works here.

The Alpine Route has a long season, because of the changes in elevation. The 10/19 report is about when you would be in Takayama.
http://www.japan-guide.com/blog/koyo16/161019_tateyama.html
There is a Nohi package from Takayama that your could take (I already gave you that link)

Last year, there were no reports of when Kanazawa was at peak, just a 11/30 report at the end of the season.
http://www.japan-guide.com/blog/koyo16/161130_kanazawa.html
I believe that putting Kanazawa as far at the end of your trip will also give the gardens the best chance to shine for fall colors. This is once again, the way I suggested you set up your route. You might include a side trip to the Kurobe Gourge from Kanazawa.

Once back in Tokyo, you may want to schedule a visit to either Hakone or the Fuji five lakes. I think the Hakone Round Course with a Hakone Free Pass may be a good choice.
http://www.japan-guide.com/blog/koyo16/161116_hakone.html
http://www.japan-guide.com/e/e5210.html

Near the Hakone area is a hot springs beach resort town named Atami. It might be a good spot to stay at the end of your trip, if you decide to do the Round Course. Atami has firework displays in the bay several times a year. One is scheduled for 11/12/2017, which is at the end of your trip. The link I am giving you for the Atami is in Japanese, and it does show the date for the fireworks. You can click on the English version of the page, but the fireworks schedule is not kept as up to date.
http://www.atamispa.com/event/hanabi/

Once again, good luck with your planning.

I'm not sure what to add but here goes. I would not worry about things being too crowded as even if it is busy not everywhere will be and Japanese crowds are very polite.

Firstly a little about me. I am British, 55 and have been to Japan 8 times, most recently in March/April this year. I am interested in most things from anime to history & modern culture. As you might imagine I have visited all the places on my itineraries.
So, a little more detail, let's see. I prefer not to move about too much but to base myself in a place and day trip so I'm not always dragging my luggage around. I think that my suggestion has a balance of cities & countryside and offers a chance to move days around to fit the weather.

Tokyo: Sensoji, museums, Ameyoko, Akihabara, Meiji jingu

Nikko: I found it a little overblown but a perfect day trip
Kanazawa: A nice town but you can see the good stuff in two days at most. Of course the main draw is Kenroku-en and the samurai quarter which is great. However I particularly liked https://www.kanazawastation.com/kanazawa-shinise-memorial-hall/

Kyoto: There is so much at Kyoto you could spend all your time there. Nara & Osaka are very easy day trips. I might skip Osaka but not Nara for the giant Buddha & deer park. I like Hikone as it is a bit off the trail, has an original castle & garden. I really liked the museum of the Ii family. However the hidden gem for me was Ryoanji with it's stone garden like the famous one in Kyoto. I was the only person there during my visit. http://www.ryoanji.jp/smph/eng/

Kinosaki Onsen: Not been here but its on your itinerary
Hiroshima: A fabulous place, so much to see. and eat :) Having a few days means you can be sure of a good day at Miyajima (Check the tide times). I found The Battleship Yamato museum at Kure very interesting & great for a wet day. Takehara has an area of preserved buildings & is a very pleasant wander. Here is someone else's travel report http://www.japan-guide.com/community/pby/report-1989

Okayama: I love this place. It is a good honest Japanese city that is not overrun by tourists. The main attraction is the Korakuen garden. But it is a great base for day trips. You can hire bicycles & ride the Kibi plain or take a ferry to Naoshima for the modern art. I hiked up to Bitchu Matsuyama castle in September & it was unbelievably hot but I saw so much wild life. I stumbled across Raikyuji temple & that was superb.

Tokyo: Stop at Himeji castle on the way. The garden next to the castle is also worth a visit even though it is modern. Shopping frenzy!!

Hope this helps. The destination guides on this website are a great planning tool.

ebaychucky - Thank you so much for including so much information for my planning. It will be very helpful.

Stan - I really appreciate getting to hear your perspective and the extra information about places you particularly liked will be great to have. We also prefer to not move around too much, it increases your flexibility and it's nice to get to know a place a little more.
As you may have guessed - this will be our first trip to Japan and I've been having trouble finding the right balance. I think the ultimate solution will be more trips to Japan. We live in Seattle so it's not too far for us, relatively speaking!
The reason Kinosaki Onsen is on my itinerary is because I really wanted to visit an onsen town that has an old Japan feeling. The other option I have been considering is scratching Kinosaki and going to Okuhida Onsen, an hour from Takayama, instead. It's in the mountains, looks small with a nice atmosphere and might have good fall color. Have you been there?
Thank you for your help.

No problem. I think you have a good plan for a first trip. Another reason not to move around too much is that it can be a bit overwhelming on your first trip & having a base allows the flexibility to do things you discover you want to see as you go. I am a solo traveller and have not been to any onsen towns. Most of them seem set up for couples or groups. I have stayed in small ryokan & minshuku and that has been good.

You have gotten a lot of nice tips, shortly I would say myself change one night from Kanazawa to Hiroshima/Miyajima. Kanazawa can be seen in one day easily if you get an early start especially if you can see something also on the day you arrive or the day you leave.
For Hiroshima and Miyajima I would reserve one full day for both.

I spent two nights in Kanazawa (well actually 3 with a day trip to Shirakawa-go) and found plenty to do. But I'm the one who's always posting how I hate dashing from hotel to hotel and prefer to stay a minimum of two nights in any one place.

Thanks for your comments. I am definitely in the group that doesn't like to rush from hotel to hotel.