Making your itinerary is probably the most important but also the most difficult part of planning your trip.
Still preparing your trip should be already a fun part, so whe are here to help you giving some structure if needed.
A structural over view.
When building your itinerary, your conditions gave give you a good starting point. So you probably already know things like, when can i go, how long can i go and also very important: What type of things i would like to see.
When starting to plan your trip to Japan it is good to keep in mind its a Island, so you probably will get there by plane or boat. This will limit your entry and departure place. Finding arrival and departure points is useful because it is wise to place these places tactically in the travel order.