There are lots of good websites on Japanese etiquette. I’d suggest checking them out, as there are lots of things to know, especially when visiting a Japanese household — taking off shoes, bringing a gift, how the bath works, etc.

Just some observations on Japan from my experience:
— The train system is fantastic. It’s as on time as trains in European countries like Germany and Switzerland, but the rail system is so extensive and well used that you’ll be amazed.
— Japanese department stores are incredible. They sell things you’ve never seen before. Try stores like Tokyu Hands and LOFT in Shibuya.
— There is a LOT more to Japanese food than sushi — try as much cuisine as possible in Japan, and you’ll enjoy it.
— Japanese people generally understand some English but are shy to use it. You’ll be most successful if you invest in learning a few common phrases in Japanese before you go.
— To see Japan, both modern and traditional, you should at a minimum see Tokyo and Kyoto, which are totally different cities. Tokyo has modern skyscrapers and urban sprawl. Kyoto is surrounded by mountains and has peaceful temples. But you should venture into the countryside as well, to see sights like Hakone, Mt. Fuji, and/or the Fuji 5 lakes.
— The streets in many cities in Japan are impossibly narrow. You can’t believe that cars pass through, but they do.

Happy travels!