Some thoughts on Japan – not esp. organized, but maybe some useful info in there somewhere, lol.
Lots of yen for the dollar now – great time to travel.
We were in Japan last fall, and I would love to go back. We had an amazing trip last fall (November) to Tokyo and Kyoto. And Kumamoto, Hiroshima, Miyajima, Kobe. Kind of a whirlwind trip. Stayed in a couple of nice hotels in Tokyo – used hotwire to get four/five star hotels there. One of the hotels we got that way was the Conrad Hilton. I love that place, though I don’t think I would ever pony up the retail price to get it. Maybe someday, when my ship comes in. 
The Kyoto hotel we stayed in was less nice, but close to the train station, and absolutely fine. Kyoto hotels were pretty booked when we went. Can’t remember how I got that hotel. Maybe through hotels.com. Hotwire, Priceline and Hotels.com are what I tend to use. Apparently everyone loves Kyoto in the fall. The train station in Kyoto is huge. We got lost in there more than once. Beautiful gardens and temples in Kyoto. We were only there for two days, and I think I need to go stay there for at least two weeks sometime. Also, the big Japanese department stores are fascinating to me. Bottom floors full of fabulous food. Actually, every place we ate in Japan had really good food, IMO. I don’t normally eat raw fish, but I do when in Tokyo, because I trust that it is extremely fresh.
We found that there weren’t always good English speakers everywhere. Esp. in Hiroshima. I think you can get by in Tokyo and Kyoto okay, though. People were very helpful, everywhere, if you just ask, and somehow we managed to communicate. One thing that might be helpful – ask the concierge at the hotel to write down in Japanese (next to your English version) the places you want to go see that day. If you find you can’t communicate, show the Japanese writing to someone, and you will have more luck communicating, and will likely be pointed in the right direction. Also, if you have to take a taxi, it helps to have your destination written in Japanese. I speak some Japanese – very little – but can get the pronunciation close if I focus, and that helps. If you aren’t pronouncing the destination right, though, no one will understand you. So, the written version is handy to have.
Do learn to say thank you and excuse me in Japanese, if nothing else. It is a very polite society.
Some of my favorite places in Tokyo – Ueno park (esp. during Cherry Blossom season) and Asakusa (lots of shops, crowded and kind of touristy, but I love it) and I also am fascinated by the 7 - 11 stores in Japan.
One of the highlights of our trip was a visit to a Japanese toolmaker located near Kobe. My husband does woodworking and has the tools made by this man. He really wanted to visit a tool maker while there. So we did. There are people in Japan who like to give tours for free (you just pay for transportation and food and, of course, give them a thank you gift, but no tips – mostly you don’t tip in Japan.) I was skeptical, but we found a tour guide through some website, can’t remember exactly which one. It worked out very well. Our tour guide was a lovely woman, and spoke excellent English and helped us ride the bus to a small town. The tool maker met us at the bus stop, and gave us a ride to his work place and showed us where he made tools, and then brought us to his house and also gave us a ride to a shopping center where he sells his tools, and where we ate lunch. My husband loved it, and I enjoyed it too.
Bring a few souvenirs or something from America to give as a gift if you are meeting anyone there, or if you end up meeting someone who helps or befriends you. Gift giving is big there. It doesn’t have to be expensive.
We had a JR pass, which was very useful. I think you have to get it before you leave the US though? Can’t remember. – Maybe another poster can advise whether I am remembering that correctly or not.