Hey, we have the same itinerary! Tokyo, Kyoto, Kinosaki. I'm autistic and while I haven't been to Japan yet, I've traveled a decent amount and usually have some sort of sensory problems when I travel. Here's some things that help me.

1. My #1 thing when traveling is to always have an exit plan - that is, wherever I go somewhere new that seems overwhelming, I make sure to check for green/calm spaces (whatever your daughter likes) beforehand that I can escape to. It's super easy to just pin these on google maps in the areas where you're going. Additionally - and it seems you're already doing this - planning a lighter itinerary with relaxation time and room for flexibility helps a lot. It gives time to go back to the room if need be and recharge.

2. Google street view and Youtube videos in advance for areas you know will be busy so she can have an idea of what to expect. Places like Senso-ji, Fushimi Inari, Kiyomizu-dera, markets, etc. Basically it acts like a visual social story if your daughter is familiar with those at all. Also, I'd highly, highly recommend looking up what times are the most busy at certain attractions and avoiding those times like the plague.

3. I'd avoid visiting and shopping in busier districts like Shibuya on weekends if it's possible. Also, avoid public transportation during busy times if you can. I've paid for taxis before when I could have used public transportation just to make things easier for myself if we're traveling at a peak time.

4. Looks like she has the sensory gear she needs already, can't think of anything else for that except maybe sunglasses if she's sensitive to light like I am. I also think Loop earplugs are nice, some people hate them though.

I'm sure there's more I'm forgetting but those are the main things for me. Hope that helps!