I lived in Tokyo for 7 years, so this is both the easiest and the hardest country for me to write about.  It’s so difficult to narrow down the ‘best’ of these places since there are so many layers that could be uncovered.  

Logistics:
Prior to travel, get a QR code from Visit Japan Travel to speed up the immigration process.

Use the Rail Pass Calculator to see if it makes sense for you to purchase a Japan Rail Pass prior to your visit — a special fare ticket that is available only to travelers visiting Japan from foreign countries for sightseeing. There are 7-day, 14-day, and 21 day passes. This pass must be purchased BEFORE coming to Japan. You can also use the Japan Transit Planner to figure out your transportation and fare. Instead of buying a subway/train ticket each time, buy an IC card (Suica or Pasmo) and just load some money on it. It will make your life much easier! 

Connectivity
If your existing phone plan does not offer a good international plan, a pre-paid SIM cards or pocket wifi are the best options. We’ve used Japan Wireless. 
Download the app “Japan Wi-Fi auto-connect”, which will automatically connect you to any free wifi available when you travel.

Itineraries / Guides:
10-Day Itinerary for first-timers

Comprehensive Japan travel recommendations in Google docs format (no photos)

Japanese food guide/glossary:  a list of the most iconic foods in Japan, with descriptions of what it is and where you should eat it