@thedoctor For bullet trains, if you want to put your luggage in a specific space behind the rearmost seats of each car, you need to make reservation for it. Otherwise I don't think any specific preparation is required.
@thedoctor As far as I know, you can't get a phone number without a proof of address in Japan in order to prevent scam calls. Docomo is known for its area coverage, but the advantage is not so big. I don't know much about short stays.