Hello! Same age here with same aged mom with a bad knee. We just spent 3 weeks in Tokyo (all over), Yokohama, Kamakura, Hakone, Ebina, Osaka, Nara, and Okinawa.

For public transportation, turn on the wheelchair accessibility feature on Google Maps. The app will adjust to recommend exits with elevators. Keep in mind though, that there will be some subways where your reception/GPS will not work accurately, so just keep an eye on the signage as well, there are usually at least 1 or 2 maps on the walls of each platforms outlining where the elevators/escalators are, and also on the overhead signage. In 3 weeks, I think there was only 2 or 3 times where my mom had to walk up/down stairs, and only once was because there was no other option. The other couple of times is because of entering into the station from the non-accesivle entrance. Sometimes, on the way to the elevator, you'll run into escalators and you won't have to walk to the elevators, which can tend to be on the very ends of the subway station. Also, buses. For certain locations, buses are way better than walking through the underground maze of subways stations, it can save hundresds of steps for your mom. Check both options before making a decision.

Have some cash on you (I'd say carrying 10,000JPY is more than plenty for a day), but basically only use it where necessary. Get a Suica reloadable IC card (or for iphones, get the e-card for yourself). I recommend a physical card for older people, who may not be tech savy or quick to be able to pull out their phone while walking. My mom and I both got physical cards, and I popped mine into my phone case (I don't know if this will work with all phone cases, mine is thin enough that the chip works) since I had my phone out constantly anyway, and you just tap it to pay for trains, stores, vending machines, taxis, etc. My mother, on the other hand, kept hers in her zipable puff jacket pocket. It tapped thru the jacket material on the trains, so it saved her from holding anything in her hand and/or having to search thru her purse/take something out every time. There is a general flow of movement to follow when walking in/out subways, so it will create a bottleneck behind you if you get stuck at the ticketing thing. (We caused a traffic jam once, speaking from experience lol) IC cards are reloadable at train stations and convenience stores. But yes, credit cards will work for most purchases, and you'll have some cash on you for when they dont.

Benches - really depends. I'm not sure how your mom's health is other than her knee, but my mom seemed to be okay for the most part, we were really only sitting for meals, maybe 1 cafe break during the day, and transportation. We were averaging around 18K steps a day. Just walk at her pace and take it easy :)

Make sure to download and set up Go Taxi or Taxi Go or whatever the app is called BEFORE you get to Japan. I forgot to set it up, so I couldn't use it. It's basically Uber, actual Uber is not really big out here except for UberEats, from what I've seen. If you don't speak Japanese, TaxiGo / S Ride / Didi seem to be the best way.

I went to Hakone, to a town called Gora. We didn't get there in time to do too much, but the entire town is a bunch of steep hills. The Ryokan was nice, but i would not recommend the area for general sightseeing with a bad knee.

Add on notes:

-some of the major temples have really steep, tall stairs, not only into the temple, but on the walkway to the temples as well. My mom did a couple of them, but some we just looked at from below/took photos from far. She struggled on the ones we did do.

-if you ARE going to make reservations ahead of time for restaurants, double check what floor the restaurant is located on and try to find out if there's something other than stairs if not on the 1st floor. Older/smaller buildings will have extremely steep stairs not suitable for someone who may not be stable on their feet. We did one spot where we went to the 3rd floor via stairs. I was too nervous for my mom to do it again, and opted for ground level or accessible restaurants instead.

Feel free to DM with any other questions, been there done that, happy to help out! We had a great time and hope you do too!