install the Japan Transit Planner app on your app store of choice for planning out how you'll travel via train
You can use willer bus (a highway bus company) for overnight journeys from one area to another. It's slower than bullet train but much, much cheaper. https://willerexpress.com/en/
And I've stayed in manga kissa (internet cafes with manga and free drinks). You can stay there overnight for a very reasonable price BUT you have to be very quiet. https://www.youtube.com/watch?v=4G48M7pmuws
@dharmadudebro Fuji Dream Airlines, a LCC, has a special price for domestic flights within Japan for visiting foreigners. That could be a way to cover a lot of ground quickly within Japan for not much money.