Its not even cost efficient to stay in Narita and travel that far even with buying the rail pass.

Its like staying in Connecticut and riding the train into Manhattan, but for tourist purposes.

LapLap's advice is spot on, but I understand how it can be daunting for a first time visit to Japan and goto places you may never have heard of. However, that is the best advice I've heard yet and you will only know that once you have been there. You will definitely get way more bang for the buck by skipping Tokyo. If you must be in Tokyo, stay in the city and try to squeeze it out. You can eat cheaply if you avoid traditional restaurants.

Staying in the Kansai region will provide the most Japan for the money.