Yes, it's fairly easy to travel by train in Japan, so no need to worry.

Most advice has already been given..... but some additional things to consider:

- You probably already know that hyperdia.com is the way to go if you are looking for which train to take. But it's also very useful in the details that are shown like which platform a train leaves from. That is very helpful since some of the stations can be a bit daunting and although most signage is bilingual, not all is.

- No need to get all your tickets all at the same time. But it sometimes can be useful to get them the day before since some routes can be busy and the occasional train might be sold-out. Hardly a problem though since the next one is normally 15 minutes later.

- Using you railpass for the Tokyo-NRT route is a bit of a waste, assuming you will be staying in Tokyo those last days. You might get better value out of it maximizing the 7/14/21 days you are actually traveling longer distances. For Tokyo-NRT an inexpensive ticket can simply be bought separately (or plenty of options for cheap multi-day / combined tickets there).

-And try to keep your luggage as small/light as possible. You will hardly have any trouble but less luggage does make for a more enjoyable trip.