So this "Itinerary" It's still more of a draft than anything, I don't even have the plane tickets yet, but I have more or less confirmed that I could make a trip of this lenght, so now I'm trying to gauge how much time will each place require. And also seeking some opinions on places I'm not fully convinced or could be missing for going solo.

Some context:
Why go on Summer? The one who was going to Japan originally was my dad, and because of his job could only go on Summer or Winter, he chose Summer.
And so when he told me he was going, I decided to go with him, at least on the same plane since I've never gone outside my country(Argentina), neither done or planned a long trip like this either, so going alone for everything was a little too much. Plus he has lived in Japan for like a year, so it was overall convenient except for the heat of summer that will surely kill me if I don't start doing more excercise now.
Still, my dad will be mostly on Kyoto for most of the time, that's why mostly solo trip.

As for the itinerary itself, I listed places of interests that I saw from youtube videos, like Abroad in Japan, and some coworkers recommendations. I'm missing listing some activities on Tokyo that I still have to research more. Also dropped places like Nikko or North Japan in general because they're more like winter or autumn places. Another clarification it's I was thinking starting just like 1-2 days in Tokyo, then kind of like Kanazawa -> Takayama -> Kyoto -> Osaka and from there somehow visit the rest of other places further down and then return to Tokyo and stay there till the end.

And the most controversial place I want opinions on is Okinawa, my dad doesn't think it's worth going, he hasn't been there despite having lived in Japan.
I'm mainly interested in trying out diving and such, although i'm not sure how it works in terms of reservations and stuff, some things require a license I read. Aside from that, i'm not really a beach/pool guy, can't even swim properly, it's been years since I've been to one.

Lastly opinions on Fukuoka and Nagasaki? I removed them at some point because I had less days in mind at the beginning.

P.S: I forgot to mention, but I have watched an absurd amount of anime, so any kind of pilgrimage that I could do while on my trip that you recommend, feel free to mention. I'm planning on visiting Kobe to see the Fate Stay/Night places like the bridge and mantions.

Probably should have made different posts, but oh well… hoping it doesn't get deleted as soon as I press post.

Total: 44 days

40 excluding airplane time (33h∼)

Tokyo – 10 Days

Main Areas

• Akihabara (1 day)
  • AmiAmi (figures/collectibles)
  • Radio Kaikan (anime/electronics).
• Shinjuku (½–1 day)
  • Omoide Yokocho – nostalgic alley with food stalls
  • Golden Gai – small bar district
  • Kabukicho – neon nightlife
• Shibuya (½–1 day)
  • Shibuya Crossing
  • Mag Park rooftop view
  • Shibuya Sky Observatory
• Roppongi ½ day – Mori Tower Observation Deck
• Odaiba ½ day  – Futuristic entertainment district
• Ginza ½ day – Luxury shopping + dining

Parks, Shrines & Culture

• Ueno Park (Zoo, Museums)
• Yoyogi Park
• Shinjuku Gyoen Garden
• Imperial Palace Grounds
• Meiji Shrine
• Nezu Shrine
• Senso-ji Temple (Asakusa)
• Tokyo Tower & Tokyo Skytree

Museums & Experiences

• TeamLab Planets / Borderless – Digital art immersion
• Ghibli Museum (½ day) –
• Nakano Broadway – Retro/anime shopping
• Toyosu Fish Market – 
• Warner Bros. Studio Tour

Food Highlights (Tokyo)

• Ramen: Menya Nishikawa (3.61), Ippudo
• Tonkatsu: Tonkatsu.JP (3.69)
• Yakiniku: Ebisu Yoroniku (4.37)
• Sukiyaki Nabe: Juniten (3.53)
• Udon: Iwashiya (3.69)
• Yakitori: Torisawa 22 (3.98)
• Unagi: Sumiyaki Unafuji (3.71)
• Teppanyaki: Kuzushi Teppan Avagura (3.65)
• Tempura: Ginza Onodera (3.53)
• Sushi: Udatsu Sushi (3.72), Uobei conveyor sushi

Tokyo Theme Parks

• DisneySea (1 day) – Unique to Japan
• Disneyland (1 day) – Classic Disney

Day Trips from Tokyo

• Kamakura (½–1 day)
  • Great Buddha (Daibutsu)
  • Tsurugaoka Hachimangu Shrine
  • Hokokuji Temple (bamboo forest + tea)
  • Komachi-dori shopping street
  • Kamakura Beach
• Yokohama (½ day)
  • Minato Mirai Skyline
  • Cup Noodles Museum
  • Chinatown
• Matsumoto (½–1 day) – Matsumoto Castle
• Kawaguchiko (1–2 days) – Mount Fuji area
  • Lake Kawaguchiko & Saiko Iyashi-no-Sato Village
  • Climb Fuji?
  • Fujiyoshida Sengen Shrine
  • Chureito Pagoda (Fuji view)
  • Fuji Panoramic Ropeway
  • Fuji-Q Highland Amusement Park
  • Syosenkyo Gorge

Kanazawa – 1 Day

• Kenrokuen Garden – One of Japan’s top 3 gardens
• Kanazawa Castle
• Higashi Chaya District – Geisha district, gold-leaf desserts
• Nagamachi Samurai District
• Omicho Market – Fresh seafood/unagi
• 21st Century Museum of Contemporary Art
• DT Suzuki Museum
• Oyama Shrine
• Tsuzumi Gate (Kanazawa Station)

Food:

• Sushi: Kirari (bullet-train conveyor, gold leaf), Mori Mori, Sushi Ippei
• Ramen: Menya Taiga (Black Miso Ramen)
• Tea Ceremony: Shigurei-tei

Shirakawa-go Village – ½–1 Day

• Traditional thatched roof farmhouses (UNESCO)
• Try custard pudding at House of Pudding

Takayama – 1 Day

• Sanmachi Suji – preserved old townTakayama Jinya – historical government house
• Miyagawa River walk
• Takayama Showa-Kan Museum – Retro Showa era
• Hida Folk Village (if not visiting Shirakawa-go)
• Okuhida Onsen stay (Yukimurasaki Ryokan)
• Shinhotaka Ropeway – alpine views

Food: Wagyu beef skewers, Bagpipe café

Kyoto – 5 Days

• Fushimi Inari Taisha – 10,000 torii gates
• Arashiyama: Bamboo Grove, Monkey Park, Tenryu-ji Temple, Togetsukyo Bridge
• Kinkaku-ji (Golden Pavilion)
• Ginkaku-ji (Silver Pavilion)
• Kiyomizudera Temple
• Yasaka Pagoda + Ninenzaka/Sannenzaka streets
• Nijo Castle
• Nanzen-ji & Eikan-do Temples
• Gion & Hanami-koji – Geisha district
• Nishiki Market – Street food
• Pontocho Alley – Ohmi beef & nightlife

Food:

• Tempura Endo, Saryo Tesshin (soba), Ramen Sen no Kaze

Day Trips from Kyoto

• Kurama & Kibune (1 day) – mountain temples & river dining

Nara – 1 Day

• Todaiji Temple – Great Buddha
• Nara Park – Deer feeding
• Kasuga Taisha Shrine
• Isui-en Garden
• Mount Wakakusa
• Naramachi – old merchant district

Food: Yomogi Mochi at Nakatanidou

Osaka – 4 Days

• Dotonbori – neon lights, street food (takoyaki, okonomiyaki)
• Osaka Castle
• Umeda Sky Building
• Shinsaibashi shopping
• Shinsekai District – retro vibes, kushikatsu skewers
• Namba Yasaka Shrine (lion head shrine)
• Tempozan Ferris Wheel
• Don Quixote Ferris Wheel
• Osaka Aquarium
• Universal Studios Japan (1 day)

Food: Negiyaki Yamamoto (3.55 – negiyaki/okonomiyaki)

Day Trips from Osaka

• Koyasan (2 days) – Temple lodging & spiritual sites
  • Danjo Garan, Kongobu-ji, Okunoin Cemetery, Kobo Daishi Mausoleum
• Nagoya (½–1 day) – Ghibli Park
• Himeji (½–1 day) – Himeji Castle
• Kobe (½–1 day) – Kobe beef, harbor city

Kinosaki Onsen (1–2 days) – Ryokan + hot spring hopping

Kurashiki – Canals ("Venice of Japan")

Naoshima – Contemporary art island

Onomichi – Shimanami Kaido cycling route

Hiroshima – 1 Day

• Peace Memorial & Atomic Dome
• Itsukushima Shrine (Miyajima Island) – Floating Torii Gate

Hakone – 1–2 Days

• Stay at a ryokan with hot spring
• Owakudani Volcanic Valley – Black eggs, Fuji view
• Hakone Shrine
• Lake Ashi Pirate Ship Cruise

Okinawa – 4 Days

• Naha – City, Blue Seal Ice Cream
• Snorkeling/Scuba Diving – Coral reefs
• Beaches –

Food: Rafute (Okinawan braised pork)