Advice on 25 Day trip March 2016

Hi I'm planning a 25 day trip to Japan in March 2016. If anyone would be able to take a look at my proposed itinerary, and make any suggestions, places not to miss, or provide advice for my travel that would be fantastic. Is everywhere okay to visit in March? I don't mind a fast pace or getting up early and having a long day to see as much as possible. I like the outdoors and am quite happy hiking and walking as well as visiting museums. This is my 2nd visit to Japan - I have previously visited Nara, Kyoto, Hiroshima, Miyajima, Hakone & Tokyo. I am also wondering whether to get a 21 day JR Pass or whether the regional passes might be better value. Thank you!

Day 1: Arr Tokyo mid-morning (probably at Narita); Overnight in Tokyo
Day 2: Day trip Kamakura; Overnight in Tokyo
Day 3: Train Tokyo - Nikko; Visit Toshogu, Museum of Art, Futarasan-jinja; Overnight in Nikko
Day 4: Visit Yumoto Onsen, walk to Lake Chozenj; Overnight in Nikko
Day 5: Train Nikko - Nagano - Yudanka; Visit Jigokudani; Overnight in Yudanka
Day 6: Train Yudanka - Matsumoto; Visit castle; Overnight in Matsumoto
Day 7: Train Matsumoto - Takayama; Visit Hida Folk Village; Possibly visit Funikawa?; Overnight in Takayama
Day 8: Bus Takayama - Ogimachi - Kanazawa; Overnight in Kanazawa
Day 9: Visit castle, 21st century Museum of Art; Overnight in Kanazawa
Day 10: Train Kanazawa - Fukui Dinosaur Museum - Kyoto; Overnight in Kyoto
Day 11: Cookery class; Overnight in Kyoto
Day 12: Train Kyoto - Himeji - Okayama; Overnight in Okayama / nr Uno Port
Day 13: Ferry Uno Port - Naoshima; Visit art galleries; Overnight on Naoshima
Day 14: Ferry Naoshima - Okayama; Train Okayama - Matsuyama; Visit castle; Overnight in Matsuyama
Day 15: Train Matsuyama - Yawotahama; Ferry - Beppu; Train Beppu - Yufuin; Visit glass msueums, Lake Kinrinko; Overnight in Yufuin
Day 16: Train Yufuin - Hita; Vist Hirose Shiryokan, see Hina dolls; Overnight in Hita
Day 17: Bus? Hita - Mt Aso - Kumamoto; Overnight in Kumamoto
Day 18: Ferry Kumamoto - Nagasaki; Visit Peace Park, Shofuku-ji, Suwa-jinja, Sofuku-ji, Glover Garden; Overnight in Nagasaki
Day 19: Train Nagasaki - Fukuoka/Hakata; Overnight in Fukuoka
Day 20: Train Fukuoka - Kyoto; Overnight in Kyoto
Day 21: Train Kyoto - Ise Shrine - Nagoya; Overnight in Nagoya
Day 22: Cookery class near Nagoya; Train Nagoya - Tokyo; Overnight in Tokyo
Day 23: Cookery class in Tokyo; Overnight in Tokyo
Day 24: Ghibli Museum; Overnight in Tokyo
Day 25: Fly home (probably from Narita)

Hollow.your suchedul is very active. I hope your make each stay to be happy.For example,do you have a plan to go to Dougo-onsen at Matuyama. I recommend you to go to dougoonsen honkan.
This is the place of models 'Sento chihiro'http://www.dcity-ehime.com/syousai/main.asp?P_MOD=2&P_TMOD=54&P_SNO=D0...
It will open 6:00am, you will go before 6:00,and you should choose 2nd floor,it needs additional fee.but I recommend that.
After onsen please eat botyandango there.
Just one advice sorry.

1. In March, weather is quickly changing from winter to spring. If you start on 1st March, you will end up on 25th when it is rather winter: no cherry blossoms. If you start on 10th, then your last day of 5th April will be in full bloom of cherry blossoms around Tokyo and Kansai region (Kyoto, Osaka etc.).

2. You should research in more detail about the transportation. For example:

Day 7: Train Matsumoto - Takayama; Visit Hida Folk Village; Possibly visit Funikawa?; Overnight in Takayama

Check the route on google map. There is no direct train from Matsumoto to Takayama. You must detour via Nagano and Toyama, or via Nagoya, which will take more than 4 hours. Instead you can choose bus route via Hirayu onsen which is shorter and much cheaper than train. You can buy a combination bus ticket Matsumoto-Takayama-Shirakawago-Kanazawa.

https://www.alpico.co.jp/access/ticket/pdf/mitsuboshiroute2014[1].pdf

3. Your itinerary is rather unique: You will travel with bus and ferry frequently. So you should calculate the train fare and examine whether any kind of travel pass is valid for your itinerary. I feel individual tickets may be cheaper.

Have fun!

What.., going to Kanazawa and neither seeing the castle or kenrokuen?? A traversity!!

Not staying in kaga onsen or yunokawa onsens near Kanazawa?

Is one day in Kumamoto enough? I don't think so.

Do you have a break day? You seem to be doing one city in a day. You won't have the time to calmly appreciate each City. You might also want to do certain cities for 2 days or stop by Nagoya. Might need a rest from all that traveling around. You can take a break on the Shinkansen but it may not be sufficient. Don't want to break down somewhere someplace

Thank you so much everyone - I have taken some of your advice. I have also had to change my trip so I will be travelling in October and November. I think that I will be running about too quickly to see anything on my original itinerary so I am going to spend most of my trip in Central Honshu. You are right and I think I am spending too much time on buses / private railway lines, so a JR Pass is probably more expensive. My trip will look more like this:

22 October Depart London

23 Arr 0635 Haneda;
Tokyo: ?
Stay: Tokyo

24 JR Train: Kamakura Day Trip: Engaku-ji, Kencho-ji, Daibutsu
Stay: Tokyo

25 JR Train: Tokyo - Karuizawa - Komoro; Bus to Asama-sansou
Climb Mt Asama / Mt Maekake
Bus to Komoro; JR Train to Karuizawa - Nagano
Stay: Nagano

26 Nagano: Zenko-ji, Higashiyama Kaii Gallery
Stay: Nagano

27 Bus: Togakushi Day Trip: walk between shrines
Nagano-Denetsu Line Electric Railway to Obuse
Stay: Obuse

28 Obuse: Explore town
Nagano-Denetsu Line Electric Railway to Yudanaka
Stay: Yudanaka

29 See the snow monkeys
Nagano-Denetsu Line Electric Railway to Nagano
Stay: Nagano

30 JR Train to Matsumoto
Matsumoto: Castle, Japan Ukiyo-e Museum
Stay: Matsumoto

31 Matsumoto: Explore more of the city
Stay: Matsumoto

1 Private Train to Shin-Shimashima; Bus to Kamikochi
Mt Yake hike
Stay: Kamikochi

2 Bus to Takayama
Stay: Takayama

3 Takayama: Hida Folk Village, Hida Takayama Mus of Art, Takayama Yatai Kaikan
Stay: Takayama

4 JR Train: Day trip to Furukawa
Stay: Takayama

5 Bus to Shirakawa-go – explore villages
Bus to Kanazawa
Stay: Kanazawa

6 Kanazawa: Kenroku-en, Castle, 21st century Museum of Contemporary Art
Stay: Kanazawa

7 JR Train to Fukui; Private Train (Echizen Railway) to Katsuyama; Bus to Kyoryu Hakubutsukan-mae
Fukui Dinosaur Museum
Bus or train? to Eihei-ji
Eihei-ji
Stay: Eihei-ji or head to Kyoto on JR Train

8 Cookery class in Kyoto
Stay: Kyoto

9 JR Train: Himeji Day Trip
Stay: Kyoto

10 JR Train to Ishiyama Stn; Bus to Miho Museum
Stay: Kyoto

11 Travel (?) to Koyasan
Accom: Koyasan

12 Travel (?) to Ise
Ise Shrine
JR Train to Nagoya
Stay: Nagoya

13 Travel (?) to Tsumago
Walk Tsumago to Magome
Travel (?) to Tokyo
Stay: Tokyo

14 Cookery Class in Tokyo
Stay: Tokyo

15 Ghibli Museum
Stay: Tokyo

16 Fly Home from Narita

May I suggest Tateyama Kurobe Alpine Route? I saw this in early Oct. 2014 as part of an organized tour and liked it a lot.