I just wanted to add a little of my experience in Kyoto and surrounding areas to give you some help planning. So you know, I used a manual wheelchair throughout the trip and my older brother was my caregiver. We stayed in Osaka for a week, using it as my HQ for visiting other areas. Not sure if it can be an option for you (assuming you’re not stuck on a tour package), but we rented a car, which a Japanese friend of mine drove for us. The roads and rules were definitely different than the US and even a bit hectic at times for my friend (who is used to the Tokyo area), so my brother was happy he didn’t have to drive.
We saw downtown Osaka on foot, so we didn’t need the car there, trains were accessible and so was the beautiful Osaka Aquarium. Drove to Nara, saw the deer and great Buddha, parking wasn’t hard to find and lots of seating (though expect the deer to come up and beg). Drove to Kobe and over the longest suspension bridge in the world, visited downtown, finding parking was more difficult so used some trains (easy to use) and had a real Kobe beef dinner (wasn’t cheap, but very delicious). Drove to Iga-Ueno, it was a historical and fun Ninja themed area, parking wasn’t an issue. Took two days in Kyoto, parking was limited and so we were often on foot, didn’t have issues getting around on the streets but most sightseeing places varied in accessibility (e.g. Golden Pavilion: compacted rock paths, Sanjusangendo: easy access but no shoes in temple, Kiyomizu-dera: Paved but has a VERY steep hill on one side). We only touched a small portion of Kyoto in those two days, but it was worth it (even our rainy visit to the pavilion). Definitely check out Accessible Japan’s Kyoto section for more info if you haven’t already (https://www.accessible-japan.com/wheelchair-accessible-travel-destinations-and-tourist-attractions-in-kyoto/).
Some things to consider if you do use a rental car:
-Book a hotel parking space before arrival (I assumed we could at arrival, almost didn’t get a spot).
-There may be limited car choices (size/model) available, we got one just big enough to fit my chair in the trunk.
-Parking may be an issue at your destinations (in Kyoto we had to do a bit of foot travel just to get to/from parking).
-Plan for toll road fees (we tried to avoid tolls on the first day, it was a significantly longer trip, so I just paid tolls the rest of the time).
-GPS may have English, but don’t count on it (our driver was Japanese so wasn’t an issue).
I hope that helps,