When planning a multi-destination itinerary, we find it useful to set it out in an excel spreadsheet and sometimes also visually on a map.
An excellent tool that I discovered when planning our Europe trip was the Eurotrip Planner. The planner enables you to tell the tool your budget, number of days and select destinations which you can edit and reorder as required. It enables you to start with a long list of possible destinations and cull it to fit your time and budget.
Even though this website is designed for European travel, I have successfully used for Japan and other destinations. If you are using it for Europe it will even tell you which rail pass you need.
Here is an example of our most commonly used spreadsheet, which you can tailor to suit your plans.