Hello Luna,
You shouldn’t need to worry about your wheelchair and most trains in Japan (if you use a scooter, it could be an issue though), the trains are VERY accessible and you’ll regularly get extra help getting to your destination which can make it a breeze! If you haven’t already, we recommend checking out Accessible Japan’s transportation section (here: https://www.accessible-japan.com/wheelchair-accessible-trains-and-subways-in-japan/). Any of the choices on the link you sent should be fine, so probably the quickest or least transfers. I would consider a JR Rail Pass for the time you’re there if you plan to do a lot of train travel (you must buy it before you go, it may cover the cost of JR lines and possibly the Shinkansen in your mentioned trip), it can make it super easy to get around.
Also, make sure to check out Accessible Japan’s Shinkansen (AKA Bullet Train) section if you decide to use one. Seats available for wheelchairs can sometimes be limited, which could possibly cause a delay, so consider getting them as early as you can. It’s best to plan ahead with it, I originally didn’t account for this myself one trip, but luckily I didn’t have a problem getting a ticket (and this was at a busier time) which would of otherwise delayed me more than an hour.
Side note: I find that Google maps provide good suggestions for trains
as well, additionally they often have 360 street views and photos of
stations that can make planning easier.
The buses you mentioned may be currently suspended due to previous Covid-19 restrictions and the current tourist restrictions requiring tour packages. I personally don’t know what kind of traveling around you can do beyond the purchased package (if any), so this may effect many decisions in your trip if you’re planning to go soon (e.g. a JR Rail Pass may not be worth it if the package limits your traveling). I’d recommend getting as much information about travel packages as possible if you plan to go that route.
If you have any additional questions we’ll try to get you some answers. Otherwise, I hope that helps,
-Justin