Actually, I priced this out for green car travel. The 7 day JR green car pass cost Y37,800. A green car round trip ticket from Yurakucho Station (one stop south of Tokyo terminal on the Yamanote line) to Kyoto was priced by one of the ticket selling machines in mid-January at Y36,200. As you pointed out, a one-way trip on the Narita Express goes for around Y3,000. A daily pass bought at a JR station allowing one to ride around their network in inner metropolitan Tokyo goes for Y730.

We were in Japan for 9 days. The first day, we bought one-way point to point tickets on the Keisei Skyliner from Narita Terminal 1 to Ueno Station for Y1,920 each, and then on the Tokyo Metro from Ueno to Ginza (7 stops down the line) for Y160 each. The second day, we bought the JR Tokyo pass described below (I think it is called the "Tozunai Pass"). The third day, we validated our JR passes at Tokyo Station and used them on days 3-9.

I used my JR pass every day I had it, and made side trips to Niigata and Nikko with it--in addition to the sheer convenience of the pass, we got more than our money's worth of train rides.

In Tokyo, you can buy a one-day unlimited ride pass on all 18 subway lines (14 run by Tokyo Metro, 4 run by Toei) for Y1,000. When we toured around Tokyo on our last day there, we bought those, and got our money's worth as we used the subway 8 different times. An unlimited ride pass on the Tokyo Metro only goes for Y710. One way tickets start at Y160, and increase based on distance traveled.

If the OP is spending much time in the Kyoto-Osaka-Kobe area, there is a "KANSAI PASS" that you can buy out of ticket selling machines for Y1,700 per day, with discounts if you buy for multiple days. This pass is good on all JR surface trains, private railway operators (there are at least 6 of these), the separate subway systems in Kyoto, Osaka and Kobe.

Most ticket selling machines have a button you can press to get directions in English.

Hope this helps.