Is a pass worthwhile?

I'm arriving in Tokyo Haneda on Nov.2 and need to get to my hotel in Nishikasai. Do you think subway or limousine bus is better?

I'm travelling to Kyoto on Nov.6 and will be there 3 days, then I'm staying in Kawazu 2 days followed by Shimoda 2 days and then back to Tokyo for 3 days. It doesn't look as if the JR pass would help me for the days I am in Kawzu/Shimoda and a 7 day pass wouldn't cover both my trips to and from Tokyo.

So my questions are:
1. Would the 7 day pass be worthwhile for that middle portion of the trip?
2. If not is there another pass that covers the areas I am going to?
3. When I travel around Tokyo what is the best pass to use?

Thank you in advance.