Your trip sounds exciting and packed full of fun stuff. Here are some suggestions and details I can provide.
-Tokyo: All the Trains and Metro can be daunting at first, but because of them it is super easy and quick to get around this mega-city. Stations can get very busy around work rush hours, but if you work around that (often the next train is a 2-min. wait) you can avoid the crowds.
-Imperial Palace: The grounds are fairly flat and has cobblestone paths, though you can go on the gravel up to the castle moat for a closer look. Some of the other areas do have hills to access but even without seeing those the area is nice to visit. Just don’t expect to access the inner grounds, they are generally closed to the public.
-Meiji Jingu Shrine: The main pathway here has a beautiful canopy of trees with paved walkways next to gravel, only issue may be that it is rather long (700m) and may be a bit of a walk before you can find a seat to rest on. The shrine itself is very accessible.
-Takayama & Shirakawago: Looks very accessible, I found some nice info here: https://www.japan-accessible.com/city/takayama.htm
-Kanazawa: Looks very accessible, I found some nice info here: https://www.japan-accessible.com/city/kanazawa.htm
-Kyoto: Mass transit trains are not as dense here, expect to get around by car, bus, or taxi. It is also more hilly than Tokyo.
-Kinkaku-ji Temple: One of my personal favorites, while you can’t go in the building itself, the outside is arguably the best views anyway. The paths are compacted gravel and shouldn’t be much of an issue (I went in the rain even and it wasn’t really an issue in my wheelchair). Part of the garden section is accessible by stairs, however, you can still see all angles of Kinkaku-ji and avoid the step-portion.
-Ryoan-ji: I wanted to visit this location, however there are many steps required to access it making it not possible for my wheelchair. I think you can avoid some steps via the parking lot, but not sure. Please let us know if this has changed.
-Nijo-jo Castle: This should be accessible, gravel being the biggest issue for most outside areas (some steps in part of the garden). Rest areas are available, you may need to cover your shoes in the temple or use a loaner wheelchair if you want to avoid that.
-Fushimi Inari Shrine: Lots of slopes and steps in this area, avoiding steps and the climb up the mountain will cut out a lot of the area, though it is still nice to see just a portion of the Torii. More access details here: https://www.accessible-japan.com/places/japan/kyoto/kyoto/attractions/fushimi-inari-shrine/
-Sanjyusangendo Hall: Shouldn’t be an issue, just have to cover your feet or use a loaner wheelchair if you want to avoid that (then take your time while seated).
Some places you may want to consider if you can break from the tour…
-Kabukiza (Ginza, Tokyo area): If you are curious about traditional Japanese theater, I’d recommend checking it out. It’s very accessible, and you can get a audio commentary device that explains the play in English (or in Japanese, you’ll see many people using them).
-Kiyomizu-dera (Kyoto): I highly recommend this temple, a section of the path getting to it is a bit steep (or stairs if you prefer), but is well worth the views from the temple. Likewise, the temple itself is a wonderful example of Traditional Japanese Architecture and design. More access details here: https://www.accessible-japan.com/places/japan/kyoto/kyoto/attractions/kiyomizu-dera/
-Arashiyama Bamboo Grove (Kyoto): This bamboo forest and the few temples along the way may interest you.
If you have a collapsible wheelchair (or can borrow one), you may want to consider bringing it along (assuming you have a caregiver to push or can roll around yourself). You can always leave it in your room if you don’t need it for the day. Other than being a mobile seat to rest your feet, you may actually find it easier to get around in the Tokyo train stations. Instead of going through the turnstiles, you’ll go to a staff desk on the side and they’ll actually ask where you’re going and assist you getting on and off your train. Plus being a collapsible wheelchair, it shouldn’t stop you from stowing it in a trunk using a taxi if necessary.
Anyway, I hope that helps,