Make sure to rent a fast car, as you will enjoy the highways in Japan. I've lived there for 3 years, and to this day I have not seen better marked and lit highways in my life. They are perfectly smooth, too!
Just a tip: when entering Tokyo, do NOT take the Shuto Expressway, it's gridlock like you won't believe. You'll be stuck up there on the raised road for hours. No kidding.
You unfortunately missed the bloom of the sakura there. If you ever see a cart selling "Yakimo", try that. It's sweet potato, unique there. I loved that stuff.