For those of you interested in my wife's far more lucid and extensive notes on our trip, I recommend:
FWIW, It may be the eternal optimist in me editing my memories, but I honestly don't think things were as difficult as she makes it out to be. Sure, it was confusing, bewildering, and possibly dangerous, (more so than my trip to Europe) but there was a little tiny column of English on the train schedule... not that we were sure we were even reading that right.
My advice: Instead of trying to learn kanji (blech) see if you can find a few pictures of Japanese train schedules beforehand and familiarize yourself with the look and where the english sections are, where they can be found, etc. Of course, this may not help you out beyond Tokyo, where a surprising amount was still in english...
That said, she's right on about the hotels. Really, who puts their major airport an hour and a half from their major city? And it's not in the suburbs either. Woods surround Narita airport. It's a very bewildering feeling for the traveler expecting a world megopolis. Wait? Are you sure we're in the right country?