Here are my tips for making your travel easier:
Internet connection is important especially if you're not familiar with the country or if you don't know Japanese. A pocket wifi is essential for communication (google translate) and for not getting lost (GoogleMap). Japan may be technologically advanced but free wifi is really hard to get. There are wifi hotspots in certain areas but I find it difficult to connect especially when I'm always in the move, so a pocket wifi is more advisable.
Train passes make traveling form one area to another easier. Instead of buying individual tickets every time you want to ride the train or subway, a SUICA or PASMO card can be used. It also saves you the hassle of counting how much you have to buy for a certain ticket to use from point A to point B. You can buy a pre-loaded train card in any station or in the airport.
Google Maps/ Hyperpedia/ Rome2Rio/ or any train app
You can get instructions on how to get to your chosen destination in English, with different routes, estimated travel time for each route and total ticket price. It also tells you with platform to get on to to prevent getting on the wrong train.
Bring a camera
Japan is a very beautiful country and camera, or your smart phone, is a must to take beautiful pictures to remember your trip. Also, keeping a picture of the place or landmark you want to go to is helpful, in case you get lost you can just show the picture to someone.
Dress for the season
Dress in thick layers especially in winter and dress lightly during summer months. Spring months can range from chilly to warm especially during May-June, so it's best to wear layers. Also, remember to wear/ bring socks since you might be asked to remove your shoes in certain places.