Actually, Japan was the easiest one for me. The Japanese are in love with convenience and you can always count on the trains, and sometimes people will even come up to you and offer to help if you look lost. As an obvious gaikokujin you'll stand out more, which can actually be a good thing if you want to meet people... and meeting people in Japan isn't like meeting people in USA or wherever because you don't need to worry about impressing them.
It might seem daunting because it is radically different, but it's very safe and people are very polite and reserved. Get the rail pass before you leave... the Shinkansen is extremely convenient. If you have a few weeks, I would recommend 2 days Hiroshima, 1 week Kyoto, a day or two in Nara, a few days in Osaka, 1 week at least in Tokyo, maybe a trip to see Fujisan one day (you can climb to the top if you want, but it's not always nice... I did it and on the train back my sinuses wouldn't stop running due to volcanic dust... but if you go, do it at night to see the sunrise), Kamakura is worth a trip and if you can do it, a day in Nikko. Most people don't get to Nikko because it's kind of out of the way and the Shinkansen doesn't go there, but it really is a work of art... when I lived in Utsunomiya I think I visited about 6 times, but you have to watch the monkeys because people get attacked.
Out of the three, it's probably my favorite... I even lived there for almost 2 years.