Hope you have a nice trip! I've also been to japan recently and I'll definitely need to go again. So much to see and I really like the japanese culture.

Don't know if you already know about this, but if you're traveling by train a lot I think you should definitely check out Eki Stamps.
They're beautiful stamps with unique designs that can be found at train stations. They often represent some aspect of local culture or landmarks.
On my trip a bought a notebook to collect them all in. Probably my favorite souvenir I brought from the trip.
Also a cool way to keep track of the different stops of a trip.