Wow, what an incredible trip! I have only been outside the country once, but I am hoping to get a few more stamps in my passport over the next few years. I did a little research for you, and these were the best tips that I found:
1. Look into a Japan Rail Pass.
Japan has a train network that goes through all four of their islands. If you purchase a pass ahead of time, for a flat rate, you can save a lot of money. Also, download the Hyperdia app. It will help you keep track of the train schedule and it is available at no cost for the first month of use.
2. Arrive in Haneda
If you haven't already booked your flight, make sure you land in Haneda Airport rather than Narita International Airport. You can get from Haneda to Tokyo in less time, and for less money, than if you went a different route.
3. Get the Google Translate App
This is a free application that will help translate from English to Japanese. The language barrier may be a little intimidating at first, but this app will help you bridge the gap and get your message across.
4. Carry a small hand towel on your person.
The bathrooms generally don't have a way for you to dry your hands, so this will come in handy.
5. Carry cash.
Many places in Japan will not accept your credit card. Therefore, make sure to take about 15,000 yen with you.