Japan

Trains: Tokyo to Yokohama using the local trains from any train station - 49m; Tokyo to Kyoto on the Shinkansen bullet train - 2hr 17m; Kyoto to Osaka - 13m.

Tickets can be booked on the Shinkensan high-speed trains at the stations or using the app. See app below. 

Note, when taking a bus you pay when getting off at the front door. Either cash or you can buy day passes.

CIDER: I did not get to try any ciders in Japan but here is an article on one Japanese cider and where to try it.

Tokyo
Uobei Restaurant (recommended by B&J) - food on conveyor belts. I tried but not exceptional.

I visited the Sumida Hokusai Museum. Excellent! I like his landscapes but not his portraits. Though the bodies show some motion at times all have the same blank facial expression - which seems to be the style in his and other portraits, especially of women. The only portraits I saw showing any facial expression were of evil fictional characters expressing anger. (To get there take the Oedo line to Ryogoku Station (E12), exit A2.)

ACCOMMODATIONS:
Park Hotel Tokyo in the Shiodome Tower was excellent. Rooms were a good size, and the restaurant and bar good. Coffee and tea were free in the lobby 24 hours, and there was also an automatic wine dispenser (3 reds and 3 whites) in the lobby that was not free at ¥1,000 (~$9.00) per glass. Besides laundry service there was a laundromat. Hotel is popular with foreigners. One downside is their very expensive breakfast (~$40!) which was an very ordinary buffet and worth the cost, so I then had breakfast every day at Yoshinoya Hamamatsucho (see below). From the hotel there is access to both the Shiodome subway line and Shimbashi JR station, all without having to go outside. To reach the hotel from Tokyo Station take either the Yokosuka [JO] (blue), Tōkaidō [JT] (orange) or Yamamoto [JY] (green) line just one stop to Shimbashi Station. Note: hotel reception is on the 25th floor and guest rooms are above that.

The Kyoto Tokyu Hotel looks interesting. I went there for an afternoon drink and it looks very impressive; it is listed as a 4-star hotel but looks like a 5 to me. Take bus 50 from Kyoto Station. There are also a few higher end hotels around Kyoto Station.

FOOD:
Regularly had breakfast at Yoshinoya Hamamatsucho, 2 Chome-7 Hamamatsucho. Inexpensive and excellent - ¥666 (~$6). Very close to Daimon subway stop (E20) on the Oedo line, only one stop from Park Hotel Shiodome stop. Yoshinoya is a large chain with outlets throughout Japan (203 in Tokyo alone).

One fish I tried was Pacific saury which was very strong, even stronger than mackerel.

Hama Suchi is a large restaurant chain and is noted to be reliable and inexpensive.

Yokohama
Cup Noodle Museum. A quirky museum that highlights the success of Momofuku Ando in creating the cup noodle which helped considerably during the food shortages in Japan after WWII. You see all aspects of cup noodles, and at the end of the our you make your own custom cup noodle to take home.

Kyoto
I did the famous Fushimi-Inari Shrine hike. An interesting walk to the top of Mount Inari through the 880 gates and the shrines along the way until reaching the large shrine at the top. It was also interesting to see the many prayers that people had left for issues such as medical problems or career concerns. The hike starts near Inari train station. Take the Nara line from Kyoto Station - takes about 5 minutes.
I visited Nijo Castle, a UNESCO World Heritage Site, which is a must see. To get to Nijo Castle take the bus to the Nijojo-mae stop. I noted two examples of balanced asymmetry: the fantastic portrayal of pine trees by the artist on wall panels, and the many delicate wooden shelves.
I went on the Hozugawa River Cruise from Kameoka to Arashiyama. (See also this Japan Guide article). Cruise was great especially as rapids that start off very tiny but grow increasingly large. And the crew (of three) are very entertaining. From Kyoto, take the JR Sagano line to Kameoka (E11stop); take the Keifuku Arashiyama train back to Kyoto. There is also a Scenic Railway (also called the Romantic Railway) that goes between Kameoka and Arashiyama that follows the Hozugawa River. You could first take the JR train to Arashiyama then take the Scentic Railway to Kameoka then the River Cruise back down to Arashiyama.
The Kyoto Railway Museum has a collection of trains and an operating steam train that you can ride. The exhibits are excellent but the steam train ride is disappointing, going only about half a kilometer, but at least it’s cheap at ¥3.

I tried the Kyoto Insider Sake Experience which is a sake tasting course paired with foods and guided by an expert. It usually includes a sake brewery tour though that was not available the day I went. Choices are 1.5hr with 7 tastings or 3hr with 10 tastings. There is also an advanced course. The experience was very good! Shogo gave a very detailed explanation of the sake making process and, importantly, the distinguishing characteristics between the various types, a lot of which depends on how much the rice is polished. To get to their tasting house, take the Kintetsu-Kyoto line (B orange) from Kyoto Station to the Momoyamagoryo-mae Station (B 08). (Note that this is a surface train that leaves from Kyoto’s Kintetsu line station which is about a 15 minute walk from Kyoto Central Station and not that easy to find. Best to enter Kyoto Station Central Entrance off Hachijō West Side.) The tasting house is about a 5-10 minute walk from Momoyamagoryo-mae Station.

Great restaurant that I did not get to try is Tominokoji Yamagishi, highly rated.

ACCOMMODATIONS:
Kyoto Tokyu Hotel, 580 Kakimotocho that I visited for an afternoon drink looks to be very high quality.
I stayed at nearby Urban Hotel Kyoto which was just okay. Room was smaller than Park Hotel in Tokyo but it includes a very good breakfast (better than Park Hotel) and has a laundromat. But a major downside is the street noise from a 10 lane street - and my room was on the street side. Also, pillows were terrible - extremely hard, and their restaurant was only available for breakfast and lunch, not dinner.

Hozugawa River Boat Cruise

Regional rail map

Local rail map

Osaka
World Expo 2025 Festival

Fujikyu train service in the Mount Fuji area; many options available. Download map PDF here. From Tokyo, take the train from Shinjuku Station to Otsuki Station, then Fujikyu train to Mount Fuji Station for view of Mount Fuji and Chureito Pagoda. Optionally, continue on to Kawaguchiko Station and take boat tour of Lake Kawaguchiko.

ACCOMMODATION
Stayed at Hotel Hankyu Gran Respire Osaka, next to Osaka Station. You can walk from Osaka Station to hotel mostly inside then via a covered, elevated walkway. There are 39 restaurants in the building where the hotel is located. (Don't confuse this hotel with Hotel Hankyu Respire Osaka nearby.)

JAPAN RECOMMENDATIONS

Sites recommend by B&J and from my research:

Tokyo
Uobei Restaurant (food on conveyor belts), Yoyogi Park, Daikanyama, Shimo-Kitazawa

Nagoya
Nagoya Castle

Kyoto
Nishiki Market, Ghibli Village. Also see recommendations from tour companies below especially Nijo Castle and Fushimi Inari Taisha Shrine Hike.

Nagoya
Nagoya Castle

GYG tours in Tokyo: Shinjuku Food Tour, Ramen Tasting Tour, Classic Tsukiji Food Tour.

Anthony Bordain restaurant recommendations (from his Youtube video):
Sushi Kara Ku (Ginzo)
Chanko Edosawa Restaurant (might try the Chanko Nabe "Sumo" Stew - very hearty)
XEX Morimoto
Mienoumi (have the Katsuo No Tataki)
Have cocktails at Bar Ishinohana

Site recommendations based on tour company itineraries

G Adventures

Itinerary Tokyo - Takayama - Kyoto (all by bullet trains)

Tokyo:
1. Sensō-ji Temple: Explore Sensō-ji Temple, a colourful Buddhist temple and the oldest temple in the entire city. Leading up to the temple the street is lined with shops selling yummy food and great souvenirs.
2. Meiji Shrine (Meiji Jingū): Visit this shrine dedicated to the 123rd emperor of Japan, Emperor Meiji and his wife. The shrine is a great place to escape the bustle of the city and wander the grounds along the wide walking paths.
3. Yoyogi Park
4. Asakusa shrine
5. Quirky Harajuku
6. Shibuya Crossing
7. From Tokyo, GetYourGuide has tours of Mount Fuji and Fuji area lakes

Takayama:
Visit picturesque Takayama, surrounded by the Japanese Alps. Take in the quaint streets of old town—lined with craft shops and sake breweries

Kyoto:
Hiking Tour from Kurama to Kibune: Transfer by train and subway to Kurama Station and begin your hike. Walk between these two picturesque, quaint villages of Kurama and Kibunein the Kitayama Mountains and follow the stone steps up into the verdant, mist-shrouded forests. Pass through the highland and visit smaller temples and search for spring water outlets flowing down the trail. Stop along the way at the Kurama-dera Temple—located atop the mountain with stunning views of the countryside, Yuki Shrine, Maoden, ending at Kibune Shrine. The total hike time will be 2.5 hours for a total of 3.9km and a total elevation gain of 584m.

APPS TO DOWNLOAD

Shinkensan Booking