You have probably already thought of this, but ArcGIS online, the simplified version of the full software, would be my first choice.
It has a bit of a learning curve at first, but once you get the basic mechanism of layering down it is pretty straightforward to do what you're asking here. ESRI, the company that produces the software, has some very useful training modules that can help you get functional with the software relatively quickly. I would suspect that UC Irvine has institutional access.
The only real issue I can think of is if you're mapping this journey onto a contemporary map (such as satellite imagery) or onto an historical one. If it's the latter, you may have to search around a bit for what is called a "base map" in ArcGIS that suits your needs. There are many user-produced base maps available, and I suspect other list members may know where to find good ones for historical Japan.
Yours,
Elijah Bender, PhD History Department Concordia College
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