JoAn

Tokyo - 3.5 days Nov 16 to Nov 20
Osaka- 6 Nights-with Day trips to Kyoto Nov 20 - Nov 26
Toyko- 2 days

How do I know which trains to take and if the JR Pass will be excepted.
The System seems a bit random and hard to determine. Can you give me
some insight.

I also need to get around in Tokyo, Osaka and would perhaps take
a day trip to Kyoto. It's important that I get around to sites
in each city.

On arrival I am staying in Shinjuku can I get from Haneda to
Shinjuku Station with JR. Pass. Please advise.