18 days Japan-itinerary & transport advice

Hi,

I am travelling with my husband for a long-awaited trip to Japan this November. We are in our early thirties and love food (most important), nature and are enamoured by Japanese culture, both traditional and modern (husband big fan of Japanese manga/anime).
After a lot of research, we've created an itinerary for us as below. Ideally, we like to travel at a slower pace, but considering that our next visit to Japan may not be anytime soon and will probably only cover regions we're not covering this time, this itinerary may seem a little rushed. But any suggestions on how doable this is or if there's anything we should add/remove are welcome.

Day 1 - Arrive in Tokyo (rest)
Day 2 - Tokyo (explore Ginza area)
Day 3 - Tokyo (Shibuya, Shinjuku area)
Day 4 - Nikko
Day 5 - Nikko half day then transfer to Takayama
Day 6 - Takayama
Day 7 - Explore Kamikochi in morning and transfer to Okuhida onsen town
Day 8 - Okuhida onsen and transfer to Kanazawa
Day 9 - Kanazawa
Day 10 - Kurobe gorge and more Kanazawa
Day 11 - Transfer to Mount Koya (Buddhist temple stay)
Day 12 - Transfer To Kyoto with stop at Nara
Day 13 - Kyoto
Day 14 - Kyoto
Day 15 - Kyoto
Day 16 - Transfer to Tokyo with stop at Kiso Valley
Day 17 - Hakone (haven't finalised whether we want to do this yet. Depends on the flights we book as unsure whether we'll stay or return on this day)
Day 18 - Depart for London

We would also love to know your thoughts on tranportation as that is proving to be quite challenging. Is there a way to do this trip with a 7-day JR Pass? Do let me know if you think a 14-day pass is more economical. I've set aside £1000 for transportation (assuming 14-day pass) but would ideally like to reduce this to a minimum without adding massively to out journey times. Would love to hear more on this.

The most economical flights between London and Japan in Nov costs GBP 392.00. Assuming to take these, here is my trial case.

11/9 T LHR 2130, a night flight, easy to sleep
11/10 F 1040 DEL 2115, a night flight, easy to sleep
11/11 S 0845 NRT 0958-1251 Nikko
11/12 S Nikko
11/13 M Nikko 1006-1419 Unazuki Onsen
11/14 T Unazuki Onsen 1008-1152 Kanazawa
11/15 W Kanazawa
11/16 T Kanazawa 0946-1228 Takayama
11/17 F Takayama 1008-1100 Hirayu
11/18 S Hirayu 1000-1025 Kamikochi
11/19 S Kamikochi 0750-1247 Tsumago
11/20 M Tsumago 0914-1318 Nara
11/21 T Nara 0918-1130 Koyasan
11/22 W Koyasan 0935-1229 Kyoto
11/23 T Kyoto
11/24 F Kyoto
11/25 S Kyoto 1032-1349 Gora
11/26 S Gora 1038-1302 Shinjuku
11/27 M Shinjuku
11/28 T Shinjuku
11/29 W Shinjuku 0802-0915 NRT 1115

This looks tough. For 18 days and 12 destinations, I just assumed the following weights.
2 Nikko
1 Kurobe Gorge
2 Kanazawa
1 Takayama
1 Okuhida
1 Kamikochi
1 Kiso Valley
1 Nara
1 Mount Koya
3 Kyoto
1 Hakone
3 Tokyo

And here are competing methods of transportation. I adopted the fastest ones in the above.

11/11 S NRT-Nikko
0958-1251 2h53m 2 5430 Keisei+JR+Tobu
1115-1453 3h38m 0 4500 Bus
11/13 M Nikko-Unazuki Onsen
1006-1419 4h13m 3 15110 JR+train
1003-1520 5h17m 3 12730 Tobu+JR+train
11/14 T Unazuki Onsen-Kanazawa
1008-1152 1h44m 1 4130 train+JR
1008-1327 3h19m 1 2550 train
11/16 T Kanazawa-Takayama
0946-1228 2h42m 2 4750 JR
1110-1325 2h15m 0 3390 Bus
11/17 F Takayama-Hirayu
1008-1100 0h52m 0 1570 Bus
11/18 S Hirayu-Kamikochi https://www.nouhibus.co.jp/wp_rnw/wp-content/themes/nouhibus/routebus/...
1000-1025 0h25m 0 1160 Bus
11/19 S Kamikochi-Matsumoto http://www.alpico.co.jp/access/kamikochi/shinshimashima/
0750-0950 2h00m 1 2450 Bus+train
Matsumoto-Nagiso
1025-1231 2h06m 0 1490 JR
Nagiso-Tsumago http://www.town.nagiso.nagano.jp/data/open/cnt/3/3851/1/bus-timetable....
1240-1247 0h07m 0 300 Bus
11/20 M Tsumago-Nagiso
0914-0923 9h09m 0 300 Bus
Nagiso-Nara
0954-1318 3h24m 3 7560 JR
11/21 T Nara-Koyasan
0918-1130 2h12m 2 2600 JR+
0918-1152 2h34m 3 1820 JR+
11/22 W Koyasan-Kyoto
0935-1229 2h54m 3 2180 JR+
0935-1244 3h09m 3 2050 JR+
11/25 S Kyoto-Gora
1032-1349 3h17m 2 12230 JR+
11/26 S Gora-Shinjuku
1038-1302 2h24m 2 2060 train
11/29 W Shinjuku-NRT 1115
0802-0915 1h13m 1 2670 JR
0727-0907 1h40m 1 1230 JR+
0720-0855 1h35m 0 3100 Bus

Basically, JR does not do good jobs around Takayama. So, forget about Japan Rail Pass in this case.
7d 29110
14d 46390
http://www.japanrailpass.net/about_jrp.html

Food:

One of the complete lists of Japanese cuisines:
http://wikitravel.org/ja/%E6%97%A5%E6%9C%AC%E3%81%AE%E5%90%8D%E7%89%A9...
Top 100 selections:
http://wikitravel.org/ja/%E9%83%B7%E5%9C%9F%E6%96%99%E7%90%86%E7%99%BE...
One of the popularity rankings:
https://gurutabi.gnavi.co.jp/i/gm101/
One only for November:
https://gurutabi.gnavi.co.jp/i/gl1/m11/

Nature:

One of the lists of Koyo spots in mid-November:
https://sp.jorudan.co.jp/leaf/migoro_11b.html

Top 1 in Tochigi (Top 11 in Japan)
Nikko Irohazaka until early November.
https://sp.jorudan.co.jp/leaf/spot_54985.html
Top 3 in Tochigi
Lake Chuzenji until late October.
https://sp.jorudan.co.jp/leaf/spot_54983.html
Top 8 in Tochigi
Ryuzu no Taki Fall until mid-October.
https://sp.jorudan.co.jp/leaf/spot_54982.html
Nikko is basically over by early Nov. Oku-Nikko should be dropped from this trip.

Top 1 in Tokyo (Top 1 in Japan)
Jingu Gaien will be good from mid-November.
https://sp.jorudan.co.jp/leaf/spot_55006.html
Top 9 in Tokyo
Shinjuku Gyoen will be from early November.
https://sp.jorudan.co.jp/leaf/spot_J0002.html
Tokyo is OK.

Top 2 in Kanagawa
Hakone Museum from early November.
https://sp.jorudan.co.jp/leaf/spot_55018.html
Top 5 in Kanagawa
Hakone Yumoto from early December.
https://sp.jorudan.co.jp/leaf/spot_55019.html
Top 10 in Kanagawa
Hakone Komagatake Ropeway (the southern one) from early November.
https://sp.jorudan.co.jp/leaf/spot_104817.html
Hakone would be better at the mountain side, not at the foot (Yumoto).

Top 4 in Nagano
Kamikochi until late October.
https://sp.jorudan.co.jp/leaf/spot_55049.html
Kamikochi should be dropped from this trip.

Top 1 in Toyama:
The operation hours of Kurobe Gorge trains will be limited after 15 Nov.
https://sp.jorudan.co.jp/leaf/spot_55029.html
Kurobe is OK until mid-Nov.

Top 2 in Ishikawa
The light up of Kanazawa Kenrokuen Garden will start from 18 Nov.
https://sp.jorudan.co.jp/leaf/spot_55032.html
Kanazawa will be better in the later half of Nov.

Top 3 in Gifu
Shinhotaka until late October.
https://sp.jorudan.co.jp/leaf/spot_55056.html
Top 8 in Gifu
Hirayu Otaki Fall until late October.
https://sp.jorudan.co.jp/leaf/spot_104827.html
Okuhida should be dropped from this trip.

Top 5 in Kyoto
Arashiyama from mid-Nov.
https://sp.jorudan.co.jp/leaf/spot_55089.html
Top 14 in Kyoto
Kiyomizudera from late Nov.
https://sp.jorudan.co.jp/leaf/spot_55086.html
Kyoto is better in the later half of Nov.

Top 2 in Nara
Nara Park from late Oct to early Dec.
https://sp.jorudan.co.jp/leaf/spot_55100.html
Nara is OK in Nov.

In summary, Kamikochi and Okuhida should be removed. Nikko and Kurobe are marginally OK. If you come in early Nov, do them at first. NRT-Nikko-Kurobe-Kanazawa-Takayama-Matsumoto-Tsumago-Kyoto-Koyasan-Nara-Hakone-Tokyo-NRT? In late Nov, NRT-Tokyo-Hakone-Tsumago-Matsumoto-Takayama-Kanazawa-Kyoto-Nara-Koyasan-KIX? Or, drop Takayama and Kanazawa and concentrate on southern parts. NRT-Hakone-Nara-Koyasan-Kyoto-Magome-Matsumoto-Tokyo-NRT. Or, NRT-Kawaguchiko-Matsumoto-Magome-Kyoto-Hiroshima-Miyajima-Osaka-Koyasan-Nara-Hakone-Kamakura-Tokyo-NRT.

Anime/Manga
http://guide.travel.co.jp/archive/list/c37304/

Kamikochi buses are only until 11/15 in 2017.
Hirayu - Kamikochi
https://www.nouhibus.co.jp/wp_rnw/wp-content/themes/nouhibus/routebus/...
Matsumoto - Kamikochi
http://www.alpico.co.jp/access/kamikochi/shinshimashima/

@Luisip

I admire your effort for such a details info ! It must be taken you much time.

Have you looked at visiting the Ghibli Museum while in Tokyo? http://www.japan-guide.com/e/e3041.html Note that tickets must be purchased in advance - scroll down for the section on buying tickets outside Japan.

A manga/anime fan not considering Akihabara as a destination? It's a little surprising!