Hi Beatrice,
For Kyoto, you can check the accessibility review of Trouble with Me podcast. It has quite a lot of information on accessible transportation, including accessible taxi contacts.
https://www.tabifolk.com/troublewithme/city/kyoto-report.pdf
There’s also a report on Osaka, if you decide to go there. Just check https://troublewithme.com and you can access the links for all the episodes.
For the other cities, I’ve been to Kanazawa and Hiroshima.
In Kanazawa, I didn’t use public transportation, besides the train to get there from Osaka, which was accessible (with prior booking). The rest, I went everywhere wheeling with my power assisted chair, so I can’t help much. There were city buses, which I think were accessible, but I cannot assure you, as I didn’t use them.
In Hiroshima, the tramway was partially accessible, as only one in three of the trains were step free. On the screens you could see if the following tramways were accessible or not. Then, depending on where you want to go in the city, some of the JR train stations are accessible and some aren’t. The Shinkansen one is. You can check accessibility for your desired station on Google Maps. Press on the station, then the More information tab and scroll to find accessibility details (sometimes there’s the wheelchair logo on them and you don’t have to scroll to see).
To go to Miyajima from Hiroshima, going by train to Miyajimaguchi station and then taking the ferry to the island was wheelchair accessible. The ferry that goes directly from Hiroshima to Miyajima was not wheelchair accessible (in 2018).
Anyway, I hope it helped a bit. I really encourage you to read the reports on Kyoto and Osaka, as you’ll learn many tips and things that are also common throughout Japan.