Sharing my experience with Transit in Narita.
My flight is scheduled to have a 1 hr 50 min layover. It arrived early but due to a medical reason, passenger unloading is delayed for 30 min. I still have about 1 hr 30 min to board my next flight. However, there is a long walk (at least 1 km) to the transit terminal. And near the end is another security check point which EVERY passenger must go through (however, there is priority line for business class+). Japan has its own standard of what is allowed and what is not. I have to dump my liquid again (if it is over 100 ml). They also spend quite a bit of time looking for my power bank. So it makes going through security very slow. In the end, I made it through security after about 40 mins. Leaving me with 50 min before boarding.
At this point, there is not much one can do. Layover time is usually determined by airline and there is usually only 1 option for connecting flight. I overheard that there is no flight in the morning leaving Japan. I am not sure what happens to passenger who missed their flight due to delays during transit.
On the other hand, as far as I see, there is only 1 shop that is open (mid day) and it sells specialty clothing. So don't expect to pass time inside the transit terminal. Only other place to spend money is with automatic vending machines.
My advice: Always buy your ticket as a single itinerary, strongly recommend with the same airline (i.e. JAL / ANA) so the airline is somewhat aware that you will be stuck if you didn't board the plane. Also, go to the bathroom before you get off the plane so you can get in line early.