I think you should stop planning going to Tokyo after serious earthquake, not only because the transportation problem but also the nuclear contaimination.....
I booked car from Eagle Tour in HK. Very reliable, pay car rental fee in HK and no need to pay in Japan. The toll fee is VERY expensive. We followed the GPS to go from Ginza to Mother Farm. It took us around 1.5 hours to get there and 2.5 hours to go back to hotel. It's very worthwhile going. The scenary in the restaurant is very good and the kids like the sausage a lot.