As for actually getting around, it's just a matter of having the right tools. I'm mostly sharing this for the benefit of anyone thinking of going to Japan.
- The landscape of transit cards is confusing, and while many of them are still accepted in various places, the existence of such a wide variety is mostly a legacy thing as far as I could tell. I had a Suica card and it worked virtually everywhere I went in Japan, though I didn't venture off the beaten path.
- The Japan Rail Pass, while not having any functional use, did make things cheaper.
- A rented wifi hotspot is an absolute no-brainer. If you travel to Japan, just get one. You can pick it up at the post office in the airport and drop it back at the same place in a prepaid envelope when you depart.
- The Hyperdia smartphone app is fantasic. You can pretty much get yourself between any two points in Japan with it, and once you've used it a couple times and understand some of the icons it's easy to tell when you need a separate pass or need to walk between platforms or nearby stations.