Buy a JR East Pass. Unlimited train travel for any 5 days in a 14-day window. U can buy the pass in the train station at the airport when u land.
http://www.jreast.co.jp/e/eastpass/
Download free Google Translate app onto your smart phone. You can download a language pack which will enable you to translate even without internet service. U just point your phone’s camera at some text or characters, and the verbiage miraculously gets translated. U can also just speak into the phone and get a audio translation-- really useful for communicating w taxi drivers.
Toyko Disney is insanely crowded. A colleague just visited w his young family last month, and they had to wait 2 hours for some rides.
Driving in Japan is fine. We rent cars there frequently. None of us speaks or reads japanese. The road signage is in english, too. Plan ahead and request a car w English language GPS.
Definitely do the fish market in Tokyo–jaw dropping. But wear crappy shoes. Not necessary to be there in the early morning for the fish auction, if u are a late sleeper. Still worth seeing w/o the auction.