Hello!
Please please please consider changing your hotel. As Tanaqui points out, it’s hugely inconvenient to haul yourself into Tokyo every day, and Narita can’t even charitably be called a tourist destination.
The JR Pass works on everything–the Shinkansen (taking you to Fuji and Kyoto) and to/from the airport (the Narita Express, which stops at Tokyo, Shibuya, Shinjuku, Ikebukuro, Yokohama and other major hubs, is a JR line), and of course the Yamanote line that circles Tokyo.
There are tons of inexpensive business hotels in Tokyo. Aside from hotels, transportation costs will add up the most, and the 5-day pass means you never need think of train fares (and the only-Japanese signage, the long-ass lines at ticket machines, the tiring slog back to your hotel each night after a day of sightseeing…)
The JR pass is one pass, not a set. You show it to the nice man at the ticket window, and he waves you through. It’s good on all JR lines (unreserved seats only, I believe; they’ll tell you everything you need to know when you come here), and it’s good throughout the country.
Walking from one Yamanote station to the next is one thing; Shinjuku to Harajuku is doable but is long, and Akihabara is way over on the other side of the line, so walking would be out–plus, with the JR pass, it’s all free anyway.
I live in Tokyo, and work in Shinjuku, btw. Give a yell when you get here, and let’s grab a beer/tea!
PS. This is my first SDMB post!