37 days trip to Japan

Will be traveling to Japan on 25th October to 30th November. I have plotted the itenaries and reserved rooms. But rooms can still make changes so any comments or suggestions are welcomed.

25th Reached Haneda at 905pm. Staying at Odaiba.
26th Odaiba
27th to 29th Disney (27th and 28th staying at Disney Hotel, 29th traveling to Kobe 7pm from Disneyland. Reach at 1201am 30th)
30th Sannomiya, Rikko, Kitano staying at Kobe
31st Sannomiya, Rikko, Kitano staying at Osaka
1st to 4th Shinsaibashi, American Village, Osaka Station, Namba, Shitennoji, Dotonbori, Universal Studio, Umeda, staying at Osaka
5th Free. Staying at Kyoto
6th to 10th Kyoto Station, Fushimi Inari Taisha, Kawaramachi, Gion, Kiyomizudera
, Hihashiyama, Kyoto Gosho Nijyojyo, Arashiyama, Kibune.
11th Going to Hikone Castle and staying at Nagoya
12th to 13th Nagoya Station, Nagoya Castle, Osu Kannon Nishi Dori, Oasis 21, Nagoya Science Museum, Shirotori Park.
14th and 15th traveling to Kiso in the morning. Magome and Tsumago. Kiso Fukushima. Mt. Ontake. Staying at Kiso.
16th and 17th traveling to Mt. Fuji. Mt. Fuji and Q Highland. Staying at Fuji.
18th traveling to Hakone. Staying at Hakone.
19th traveling to Yokohama at night. Staying at Kannai.
20th Full day Yokohama. Staying overnight too.
21th traveling to Tokyo at evening. Staying at Tokyo.
22th to 24th Shibuya, Harajuku, Omotesando,Yoyogi Park, Ikebukuro, Shinjuku, Kabukicho.
25th travelling to Nikko. Staying at Nikko.
26th travelling back to Tokyo at evening or night.
27th to 29th Ueno, Akihabara, Ameyoko, Ryogoku Kakugikan, Tsukiji, Ginza, Tokyo Station, Tokyo Sky Tree, Asakusa, Sensoji.
30th flight back to Msia at 1045am.

Hotels reserved costs around USD 3350 for two of us. It is quite expensive due to staying 2 nights Disney's character room and 2 nights at luxurious ryokans. Should i buy JR Pass? How much will i need for food? Any ways to save up for transportation?

I like to visit places such as Kiso. Traditional Japan areas. But not too much of Shrines and Temples. Wanna take my girl to do lots of shopping too. Not to shop Pradas or Guchis, wanna shop japanese items, boutique shops that can only b found in japan. Any add ons to my itenaries are welcomed. I don't wanna pack too much itenaries till we get too tired everyday so i might lose some also. We are also very interested in the Muscle park such as Sasuke park. Any similar places also pls do recommend. We are from Malaysia. Also, quite interested in technologically advanced places, malls, shops, etc...

Any help appreciated.

JR Pass: No.
Shopping: Department Stores in Osaka, Tokyo, Kobe, Kyoto etc
Kyoto old streets has traditional craftworks that may be interesting
Transport: No way to save. You can use coaches instead of trains. They take longer but are cheaper. A Kansai Thru Pass may be worth while if you rearrange your days and travel a bit more in Kansai

You do not need 2 days in Kobe to cover all that. 1 day and 1 night is sufficient. You could even go up mt Rokko at night, descend, and then go to Osaka for the night.

You might want to view some gardens. Japanese architecture is serene and wondrous. I support visiting the temples and shrines in Kyoto. The ones at other cities are seldom comparable. Instead a visit to a Japanese garden may be interesting. Kokedera? Imperial garden? Okayama?

If you can include Hiroshima somewhere, then the 14 days JR Pass would be good for you to travel from Tokyo to Kyoto/Osaka/Hiroshima/Kobe/Miyajima/Uji/Nara/Nagoya and back within 14 days.

Hakone + Fuji Lakes can be done separately