I visited Japan ~4 years ago (holy shit... it's been a while), and I had a blast. A lot of the signs for trains are in English, so it's not too bad navigating. Also, a lot of people know some English. They're not fluent, but they might be able to speak some. It is, however, more likely that they'll be able to read/write it a bit better.
The flight is a bit of a pain in the ass, especially being in economy seating. Airplanes are so packed, and the seats don't recline nearly enough.