Things the guidebooks don't tell you about Japan
There are no trashcans along the road, except at convenience stores. There are only can recycling bins in front of the drink vending machines. You're expected to either eat your food on the spot, or take it somewhere and carry the trash with you home.
Oh, and walking while eating is generally rude (though somewhat acceptable in certain areas with expats), but just try to be aware of that as you're going around.
Japanese are polite and generally silent. This is particularly obvious on trains/subway lines. Don't be that obnoxiously loud person... and don't call people while on the train.
All those places famous for ancient sites? (Think: Nara, Kyoto, etc) They're still bustling, modern cities. So don't miss out on observing how they're able to merge new with old. Also: you're more likely to find actual Japanese people who are locals not at the tourist sites. So just know what you're looking for. The best piece of advice about visiting touristy places: go when no one else is there-- eg. the crack of dawn.
Japanese people do not necessarily know English, or even enough English to convey to you directions or information. Unless you're conversing with someone in English already, most folks will assume (if you have Asian features) that you can speak the language, and will not necessarily ask if you need help. Fluent English speakers are only present in major cities, like Tokyo.
Google Maps will save your butt (even though you can't save any of Japan offline). So, that's one reason to have data/cell service in Japan, especially if you are traveling to places only Japanese tourists go to.
Google Translate is also useful. The image recognition stuff is somewhat useful for figuring out what signs say. But when in doubt, find someone who can kind of understand you. (And learn a bit more than hello, goodbye, and thank you in Japanese.)
If you're seeing more than Tokyo, get a Japan Rail Pass (only available outside the country). If you aren't using it when you get to Tokyo, I suggest going to the JR ticket counter for the rail passes in Tokyo Station. The line is shorter (by a lot), but if you have time to spare at the airport, you can also exchange your pass there.