Here I will write the possible places we will visit in each city:

In general to find GF places in Japan: https://glutenfree-restaurant.com/

In general to find the train timetable: http://www.hyperdia.com/

Guide about the JR pass: http://www.japan-guide.com/e/e2361.html

Tokyo

Eating

• Glutenfree cafe littlebird
  • Address: 東京都渋谷区上原1-1-20 JPビル 3F Shibuya-ku, Tokyo 151-0064

  • Website: http://www.foods.thinknext.co.jp/en/GFinfo/

• Soranoiro (GF/Vegan ramen)

  • Address: http://osm.org/go/7Q5n~ebI9--?m=&relation=4243739

• Afuri (GF-vegan ramen ask for konnyaku men noodles)

  • Address: http://osm.org/go/7Q5nh4aVY--?m=&node=3307021787

• Natural cream kitchen (50cm sweet roll)

  • Address: http://osm.org/go/7Q5nxKPv8?m=

Shopping

Location of 100 yen shops in Tokyo Yamanote line: http://www.jnto.go.jp/eng/arrange/travel/practical/100yen.html

• Mitsubado (cosplay! for cheap!)

  • Address: http://osm.org/go/7Q54ND4sR--?layers=H&m=&node=4069489666

  • Website: http://www.mitubado.com/46_101233.html

• Animate

  • Address: http://osm.org/go/7Q54NIyZU--?layers=H&m=&node=1996594184

• Don Quijote (Biggest cosplay place)

  • Address: http://osm.org/go/7Q54NI9TN--?layers=H&m=&node=1996594184

• Mandarake Nakano (anime & comic goods)

  • Address: http://osm.org/go/7Q5yQzOyk-?m=&way=51979646

• Pokémon Center Tokyo

  • Address: http://www.openstreetmap.org/node/3350332481#map=17/35.72883/139.71916

Kyoto

Guide to reach places in kyoto by train: http://jprail.com/destinations/kansai-area/guide-to-take-trains-in-kyoto-how-to-choose-the-best-route-by-train-to-get-the-major-spots.html

• Kyoto International Manga Museum

  • Address: http://osm.org/go/7QHQzRsdA-?layers=T&m=&relation=4225854

  • Website: kyotomm.jp
• Nishiki Market

  • Address: http://osm.org/go/7QHQylZSs--?layers=T&m=&node=4170367989

• Takashimaya Basement Food Floor

  • Address: http://osm.org/go/7QHQyq0v?layers=T&m=&relation=357794

• Pontocho Alley (prettier by night!)

  • Address: http://osm.org/go/7QHQ4TcE?layers=T&m=&relation=357794

• Geisha district

  • Address: http://osm.org/go/7QHQ4L1K?layers=T&m=

  • Tram stop: Gion-Shijo

  • Website: http://www.japan-guide.com/e/e3902.html

• Kiyomizu-dera Temple

  • Address: http://osm.org/go/7QHQua0R--?layers=T&m=&way=336641107

  • Tram stop: Gion-Shijo
• Visit the Ninen-zaka and Sannen-zaka Preserved Lanes that lead down from the temple
• Ishibei-koji Lane
• Kinkaku-ji Temple (Golden Pavilion)

  • Address: http://osm.org/go/7QHRMbi?layers=T&m=&way=98115917

• Gion Corner (the show is a highly concentrated introduction to several traditional Japanese arts and include short performances of a tea ceremony, ikebana, bunraku, Kyogen comic plays and dances performed by real maiko)

  • Address: http://osm.org/go/7QHQt1i4?layers=T&m=&way=349681060

  • Website: http://www.kyoto-gioncorner.com/global/en.html

  • Coupon: http://www.kyoto-gioncorner.com/coopon.html

• Toji Temple (Japans largest pagoda)

  • Address: http://osm.org/go/7QHQgAczA-?m=&relation=357794

Eating

• Mumokuteki Café (vegan/vegetarian)

  • Address: http://osm.org/go/7QHQy5XSB--?m=&node=4545936090

• Choice (チョイス） (vegan and gluten free)

  • Address: http://osm.org/go/7QHQ5OkDR--?layers=H&m=&node=4550028390

• Organic house Salute (サルーテ) (vegan not sure if GF)

  • Address: http://osm.org/go/7QHQhtm~F-?m=

  • Website: http://da-maeda.shop-pro.jp/?mode=f12

• Macrobiotics Prunus (in Arashiyama in case we decide to go to the mountain call to prepare GF one day ahead)

  • Address: http://osm.org/go/7QF62_~vM--?layers=T&m=

Osaka

How to move around Osaka: https://www.japan-rail-pass.com/japan-by-rail/travel-tips/osaka-loop-line

Osaka Castle and Park, Dotonbori, Amerika-mura, Shitennoji Temple.

Eating

Nara

• Daifuku deli stall
  • Address: there is a supermarket under the station (sub-level), Before you go down the escalator from the station to the supermarket, you walk through a concourse with lots of little deli-style food stalls. On your left, directly after you enter this area, and before the escalators, is a stall that sells fresh daifuku and mochi.

Hiroshima

• How to access to Miyajima from Hiroshima

  • http://jprail.com/trains/sort-by-type/local-lines/how-to-get-miyajima.html/comment-page-3#comment-264219

• Tourist Loop Bus, Meipuru-pu bus stop

  • http://jprail.com/travel-informations/basic-informations/station-information/hiroshima-station-guide-how-to-change-the-trains-shinkansen-and-local-train-to-miyajima-how-to-catch-tram-and-loop-bus-meipuru-pu.html

Eating

• Shanti Yoga Vegan Cafe (Buddhist vegan cooking)

  • https://www.happycow.net/reviews/shanti-yoga-vegan-cafe-hiroshima-73516