I like to take my time while traveling so I didn't do nearly as much as is listed on the visit japan model course. If you already have a JR Rail Pass, the transit pass isn't worth it.

I was in Japan for 9 days, but only had a 7 day JR pass. We explored all the JR accessible areas first, then saved most of the subway travel for the last 2 days. We walked quite a bit and took the subway 4 times a day at most (probably because we didn't have an unlimited pass).

You can buy subway day passes from the ticket machines if there are days you plan to move around a lot. Toei line only is 700 Yen per day. Toei + Tokyo metro is 1000 Yen per day.

http://www.tokyometro.jp/en/subwayma...outemap_en.pdf