Nissan HQ in Ginza was alright if you want some rare Nissan gear or mementos.
I pretty much caught the JR everywhere and took the shinkansen from Tokyo to Hiroshima which I would definitely recommend as stated above, go see the war memorial they have and if you're lost just hop into a taxi and ask him to take you to the A-Bomb Dome, taxis aren't that expensive in Hiroshima compared to Tokyo.
I also took the shinkansen to Kyoto, went and saw this awesome castle owned by some shogun, it had floors that would creep and squeak as you approached the main building to warn the shogun of incoming assassins, it was a very good historical experience.
By the way I pretty much did this not knowing a word of Japanese, it was quite easy if you stay at a nice hotel and get the concierge to help you out, she wrote down on pieces of paper where i wanted to go and I would just show them to train officals if I got lost, but having a travelling companion who speaks the language will make things so much easier.
On the final leg of the trip I took a flight from Tokyo to Hokkaido then a bus to Niseko and went skiing, pure white beautiful powder snow if you're into that, but that was in January.