Indoor shoe etiquette reconstructed leg

I have a reconstructed ankle which causes a hard time walking without a lot of pain and limping when not in shoes with the correct heel elevation. Aside from the pain and discomfort of just the walking, after a day or two of limping, it throws everything out of alignment and my back goes out, so we'd obviously really prefer to avoid this.

My partner and I are hoping to plan a visit and we'd like to be appropriate and respectful of the etiquette and customs when visiting, but I'm also wondering if there are options or exceptions made for those with medical issues such as mine which greatly benefit from shoes. Are there medical indoor slippers I could get? I tried googling and didn't turn up much. Would having a brand new indoor only pair of shoes be acceptable if they are aware of my condition (and/or I leave my lower leg uncovered by clothing so all the scars I usually prefer to hide show so it's blatantly obvious I've got issues)?

The answer would likely depend on the specific facility you're visiting. In broad terms, there are two reasons people in Japan remove their shoes indoors. One is to keep the floor clean (since your shoes pick up dirt and grime from the ground as you walk around outside) and the other is to protect certain types of flooring (wood floors and tatami reed flooring) from scratches.

If outside dirt is the only concern, some sort of supported slipper or shoe might be OK if it hasn't been worn outside and has been kept clean, but if the concern is about footwear itself damaging the flooring, the facility might require all guests to be in only socks or barefoot.

You'll likely need to explain your condition before any place that normally requires guests to take their shoes off will grant you permission to use a slipper/shoe. Because of that, you might want to try to contact places you're hoping to visit ahead of time (or have your hotel concierge contact them) and confirm their specific policy.

「My partner and I are hoping to plan a visit and we'd like to be appropriate and respectful of the etiquette and customs when visiting」

While there are places in Japan that require you to take your shoes off when entering, this actually isn't as common a situation for travelers as you might expect. The primary place Japanese people take off their shoes is when entering a home, but you're unlikely to go to anyone's house or apartment if you're just in Japan as a tourist.

Some restaurants require you to take your shoes off at the entrance if they have delicate flooring, but many do not. In particular, casual restaurants that serve, for example, ramen, conveyor belt sushi, teishoku set meals, gyudon beef bowls, and the like don't require you to take your shoes off, for example. No-shoes policies are most common at izakaya pubs and fancy classical restaurants, but in either case you won't be walking very long distances while inside the restaurant.

Shops and shopping centers pretty much always allow you to keep your shoes on, as do museums, unless they happen to be inside of a traditional building that itself is a historical asset. Even when visiting temples and shrines, there's a chance you'll have your shoes on for the entire visit, since at many temples guests spend more time outside the buildings than inside them. For example, at Tokyo's most famous temple and shrine, Sensoji and Meiji-jingu, the public spaces guests move about in are all shoes-on spaces.

Just carry a clean bag and put it over your shoe when entering a place you need to take shoes off for. In rain, be sure you wipe water off your shoe so that the bag wouldn't leak.

But at the same time, it is also quite easy to avoid place where taking off shoes are required, be it hotels, restaurants and tourist spots such as museums. For example, you can enjoy many shrines and temples without taking off your shoes.

Take care, be safe, and let's hope you'll have fun in Japan in the near future.

You can also buy shoe socks to prevent damage to floors. They are a commercial product similar tp using a bag.

I suppose the other poster is talking about something like these.
https://www.google.com/search?q=%E7%BE%A9%E8%B6%B3%E3%81%AE%E4%B8%8A%E...

Late to the discussion, but your trip will be some time off yet. I have some experience with this having had people that cannot walk without shoes on hard floors due to feet issues, all the way up to a guest with a false leg.
For the people with foot issues they did what many Japanese people do and carry indoor shoes/slippers - the ones my guests used were mainly stiff soled slippers and were fine in the few places where shoes were required to be removed. But typically there are not too many of those - Nijo Castle is the main one that springs to mind. It has been a while since I visited a restaurant where shoes-off was required, and while they certainly exist, there are lots that do not require it.
For the guy with the artificial leg, I recall that in one particular case he did, literally put his shoe into the provided shoe carry bag, and just wore the bag on his foot - the staff understood that his getting his shoe off was going to be a major issue.
Also, you are unlikely to be visiting a home, and if you are at an inn with tatami mat floors, I doubt you would be doing lots of walking in your room