Here are some of the facts to know beforehand, ensuring your travels in Japan as a tourist are the very best.
Japan Rail Pass
Traveling as an individual in Japan for tourism, there is no question, traveling by rail ois a very good option. If you decide to travel longer distances then the Japan Rail Pass is a must (already a return trip from Tokyo to Kyoto costs as much as a two weeks JR-Pass). With the JR-Pass you can travel not only with the Shinkansen but all the other Japan Rail trains, ferries and buses.
Very helpful is a data sim card that you should use in your mobile phone for a full flat rate. But during my travels I was never tempted to phone (as only few people were able to communicate in English) but I always used helpful apps like: Hyperdia (aid for travelling by train – gives you exact information about the timetable, platform etc.) Google Maps: for finding the places of accommodations. The sim-cards you can get in many shops in Japan are cheap but you should know that they don't cover all the areas you want to travel (as most people`s English is so limited – it is wise to get the information before traveling.
You will need Wi-Fi to start the sim-card. The company Japan-Experience can help you with a bit more expensive sim-card than you can get in Japan but the card will be sent to your home address and you can prepare the set up at home and the sim-card covers all Japan.
We never needed to reserve seats on the trains and always found seats (on the very busy routes it might be useful if you know what time you want to travel). Non-reserved seats are always in specified and signed carriages and not scattered over the whole train. Hyperdia provides you with all you need to know on the information boards on the platforms or marks on the platform floors tell you about the carriages that are non-reserved carriages (always the carriages 1 to 3 or 1 to 5 at the Shinkansen trains). That means that you do not have to search the free seats on the train and you are secure knowing that the seats cannot be reserved while traveling.
Safe Traveling by Rail
Though most helpers at the stations cannot speak English there are always people there who are eager to support you and you will never be lost or unsafe. But if you ask for support you should allow the fact that it could take some time because the helper will make your problem his problem and will put all his energy into being a help.