It may be an option:

Kawaguchiko Station –(Fuji Kyoko Bus)– JR Gotenba Station — (JR Train)–Matsuda Stn. –(walk 3 min.)–Shin-matsuda Stn. –(Odakyu Train) — Odawara Stn. –(Hakone Tozan Train)–…

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There is a bus connecting from Kofu to Kawaguchiko. Their buses are all accessible (can accommodate one wheelchair or two) as far as I checked with the staff today on the phone. It takes 70-80 minutes from the JR Kofu Station to Kawaguchiko Station, 10 buses per day from departure (Kofu Minami Station) at 7:40…

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Both Tokyo Metro and Toei Transportation say all the stations are accesisble.

https://www.tokyometro.jp/safety/barrierfree/progress/tozai/index.html

https://www.kotsu.metro.tokyo.jp/eng/guides/wheelchair/
As for JR train stations in Tokyo 23 Wards, there are a few. You do not need to worry normally.

Hi, if your booking is a “normal” room, it is in many cases difficult to change it to an accessible room keeping the reservation. I think you need to book an accessible room through hotel’s direct booking site. There are cases that they do not show an accessible room on their own site and in such a case you need to book it by phone or by…

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Hi, we are travel agent with accessibility support staff. As the number of English speaking personnel is limited, the miscommunication would lead to a mishandling and, possibly resulted in a significant incident, the number of personnel who are able to do the service to non-Japanese speakers are limited though. Still we can talk to you if…

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