So my wife and I are going to be in Japan for the first time, and have been reading up on Japans transportation, but we are still a tad confused.

Our plans:

Arrive in Tokyo at NRT
Stay in Tokyo for 4 full days
Then take the Shinkansen to Osaka.
Stay in Osaka for 4 full days with day trips to Kyoto and possibly Kobe.
Then fly out of KIX to China.

From what we are gathering we need to get the JR pass, which we have to buy before we are in Japan, but it might not be worth it as we are only taking a longer trip one way? However, the JR pass will not cover all subways within cities? So we may have to buy day passes within cities?

Can anyone tell us if the JR Pass will be worth it? And any other suggestions on how to best take advantage of Japan's public transportation?

Thanks so much!