I visited Japan 4 or 5 times with a friend who's a wheelchair user (T8 paraplegic). I thought we wrote a trip report about Japan, but can't find it. I did, before our first trip, start a thread about hotels in Tokyo. At the time, my concern was more with ease of moving around the city than accessibility features of the room.

The Cliff's Notes version is, there's nothing to worry about. You will find everybody in Japan to be incredibly friendly and helpful. All train and subway lines are accessible, even though some stations are huge, confusing, and under-elevatored. Look at maps and allow a bit of extra time. Reserve seats where possible (long distance trains and airport express) and ask to be directed to the exact spot where wheelchair spaces are located.

As for hotels, accessible rooms do exist, but are far fewer in numbers than what US ADA requires, and the design standards seem to vary more widely. We generally stayed at upscale hotels (using points) -- Conrad Tokyo, Grand Hyatt Tokyo, St Regis Osaka, Ritz Carlton and Intercontinental Okinawa, and only a few midscale hotels (Westin Kyoto, Hyatt Regency Tokyo, Sheraton Hiroshima, Grand Hyatt Fukuoka, Doubletree Naha). The issue at the upper end hotels is that accessible rooms are often marketed as suites (due to their larger square footage), and can thus be very expensive. One can, of course, show up on the day of arrival and hope to be assigned the accessible "suite" (especially when holding elite status), but that carries the risk of the room being unavailable. We had a wide range of accessible rooms, including some of the best designed ones we've seen worldwide, and some head scratchers. At St Regis Osaka, the accessible room had a grab bar on one side of the toilet, and nothing else in the room was accessible. Westin Kyoto has a standard room in the basement designated as accessible room, and a secret doorway opens into a fully tiled bathroom that looks like the awkward offspring of an ill-advised romance between a 1960s hospital and a freeway rest stop bathroom. The more recently built hotels were quite good. Do note that doors of regular rooms (especially within the room, e.g., bedroom-bathroom) are often not wide enough to accommodate even modestly sized wheelchairs.

All hotels had accessibility equipment readily available, although communication was a challenge in some cases. I would recommend bringing a picture of the shower chair you use at home, so you can show them what you are looking for. At St Regis Osaka, our request was initially met with the delivery of a chair/potty for infants. Most of the hotels had shower benches (without backrest), which is very challenging for someone paralyzed from the chest down, but sounds like it wouldn't be an issue for the OP. Other types of equipment like portable toilet grab bars were available and sometimes set up proactively (even though they were a hindrance in our case and we had to ask to have them taken down again). If you can walk short distances on crutches, you shouldn't have any problems at all.