I just got back from Japan recently. Fuckin love that country. It's my #1. Tons of tourists there this year though -- I think 4x the average.
If I have one piece of advice that you prob haven't already heard, it's to stay at Hotel BaliAn Shinjuku Honten when you're in Tokyo. Yes it's a "love hotel" but really it's beautiful, spacious, clean, great location, cheap, and they throw in a bunch of freebies like as much wine as you can drink, and you can take as many facial masks, sponges, tongue scrapers, eyebrow pluckers -- fucking everything you can think of -- as you like. My wife is picky when it comes to accommodation and she said it was the one of the nicest places she'd ever stayed.