Hi! I run tabifolk – glad to have you here!

Yes, you can rent vans with ramps out of the back at various rental places. Be sure to check if it can hold your power wheelchair though as they may be smaller or have a lower roof than expected. Also, some places may not let you rent in one place and return it to another place.

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You can send us a request here! https://www.accessible-japan.com/renting-wheelchairs-hoists-japan/

Hello,

Disability certificates are really only useful for tourist sites, not the train.

For a local train, no reservations are needed, you can just show up and ask for assistance.

For the Shinkansen or other reserved seating trains, you will need to book in advance. Having a translation of your disability letter can help, but not…

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I have never been but @joanp may have.

In addition to @jul suggestion of Nakano Broadway, Ikebukuro has become another popular anime spot.　

In general, all of the places have shops that are cramped and inaccessible, those that are accessible, and places in-between.

It’s possible.
https://support.go.goinc.jp/hc/en-us/articles/25883320478745-What-is-Ride-Preferences

But it’s not perfect options because of wheelchair specifications and driver’s skills to set up ramp. Additionally taxies would be Japan Taxi, not Van type vehicle in most cases.
https://global.toyota/en/jpntaxi/