Here are some tips to navigate this extraordinary place...
There is not a great amount of English spoken by locals so be prepared with hotel and place names on your phone or written down to show people when you ask for directions. Having data available on your phone to use google maps is essential
Expect everything to be in Japanese characters, rarely supplemented by English. You work it out, eventually but it is challenging and at times ordering food at a true local is a lucky guess
Work out the cost of your inter-Japan travel you expect to do before you go - if you don't expect to do a lot of travel between cities, buying trips on the go when in Japan may be a cheaper option. As an example, our 13 day trip travelling Tokyo-Kyoto return, Kyoto-Hiroshima return, Kyoto-Nara return, Tokyo-Nagano return, made buying a JR Rail Pass much cheaper. Note that while some metro lines in the big cities will let you use your JR Rail Pass, a lot won't, and you'll have no other option other than to buy paper tickets for those inter-city trips.
If you work out that buying a JR Rail Passis the most economical option, buy it before you leave for Japan (7, 14 or 21 day options) and allow two weeks for it to be delivered (mine came within days). It may seem like a big upfront cost, but if you are travelling a lot it will end up being cheaper
When travelling with your JR Rail pass, remember that only the JR East Japan Rail Company trains are the trains you can use with this pass - so make sure you get on the right train - look out for the "HIKARI" trains. You cannot travel on NOZOMI trains with your JR pass - the stewards do come around onboard and check your tickets
The Shinkansen is the fastest bullet train so use them for long trips
Reserve train seats for trips on main Shinkansen lines in advance of travel but often the unreserved cabins are not full
Don't be afraid to spend a lot of time exploring Japan's train stations - they are vast! Some of the best places to eat are in Kyoto and Tokyo train stations - check out my Kyoto and Tokyo posts for the places we ate at and loved - KYOTO STATION / TOKYO STATION
Breakfast is sometimes hard to find so don't underestimate the sushi from chains like Family Mart and Lawsons, where you can pick up great tasting sushi for ¥120 - it can however be a flavour lottery as good luck reading the packet
Book hotels near train stations so you can easily walk to-and-fro for inter-city and suburb travel
Take an umbrella with you everywhere you go - you can buy one at the many stalls that sell them when you first arrive
Starbucks is the safest bet for coffee fixes - the other places we found served very sweet coffee
Check out reviews on what to eat and where to go in