There is no mystery to plan any international trip, but Japan has a few characteristics that deserve a little attention.
First, the big internal tourism makes high-season often completely booked far earlier than other places. While it is perfectly possible to arrive and find a place to stay, the best cost/benefits, or "that" place you wish to stay, will require a couple months, if not more, of advanced booking.
Second, Japan is actually a big country in the number of cities and places to visit, so if you want to know more than just Tokyo or Osaka, or whichever place you are landing into, you will be making a lot of trips internally, and while normally it would mean just pay and go, the main Japan Rail Group offer very nice Passes and plans to give you some worthy economy. Using such passes you can easily save more than half the cost if you didn't plan on them.
That being said, here is a simple checklist-guide for an uneventful trip.
Research and choose the best time for your trip - important if you want to avoid crowds or go in a specific season
Research and choose which trips you wish to visit - important to start the math on savings and itinerary
Find out if you can do daytrip to nearby (like 2h away) small cities - a very nice use for the passes that give you unlimited travel
Make sure your "must-see" places will be open on the day you want to visit. A lot of places close one day of the week (usually a weekday, monday is a normal closed day)
Find the stay model (Hotel, AirBnB, Hostels, Ryokans) and area you wish to stay, and start booking as early as possible (3 month for normal time, 6 month for high season)
Check which passes (if any) might give you the best value and savings. Remember: the JR passes are meant for long-haul trips (between towns), not for metro/subway. For local trips and metros there are local passes on each location that often offer some savings or just convenience.
Check if you require to purchase your pass before going to Japan for the extra discount. As of March 2017, you can get the JR (nation-wide) Pass in Japan too, but it costs about 10% more.
Check if you need to carry any controlled substance (medicine) and if you need a special permission (the so called "Yakkan Shoumei")
Make sure you can either withdraw money from Japanese ATM with your card, or carry cash. Japan is a very cash-oriented economy.
If you want internet on-the-fly, check if your carrier works in Japan, or choose among a wide variety of SIM-card plans or pocket-wifis. Otherwise, pretty much all hotel and AirBnB have WiFi you can use.
Don't forget power adapters!
We have some tools to help you around: