To Omotenashi,
Thank you for your clarification. I suppose it slipped my mind. (A lot of things slip my mind these days.)
To Matimu,
Perhaps you should contact a travel agency near you to discuss your itinerary and purchases. That's what I usually recommend to people who get confused when planning their trip. But if you're interested, please feel free to read what I wrote below.
First of all, remember that "passes" allow limitless travel within a certain area and date. Meanwhile, anyone can buy "tickets" at the spot, each time when board a train/bus to travel from one spot to another. So passes can save you money only if you are using transportation as frequently as the pass is designed for. And there are numerous types of passes depend on how you prefer to travel.
I'm going to assume you're using the "7-Day Ordinary Japan Rail Pass" which costs 29,110 yen. Details of the pass are written in the following link.
http://www.japanrailpass.net/en/about_jrp.htmlNow, there are many railway companies in Japan. In Tokyo alone, there are more than 10 including JR, Keikyu, Tokyo Metro, Toei, Tobu, Keisei, Seibu, Keio, Odakyu and Tokyu. Each company has a different fare system for its many train/bus lines.
The Japan Rail Pass basically only allows you to ride transportation operated by JR company, with a few exceptions. Among the exceptions is, as suggested by the other poster, Tokyo Monorail. The Monorail to Haneda is not run by JR, but you can use Japan Rail Pass for it. Meanwhile, there are many ways to get to Haneda. Among them, the following are 2 examples.
(A) From Shinkansen, change trains 2 times. You can use the Japan Rail Pass, so no additional charge is required.
(B) From Shinkansen, change trains only 1 time to a Keikyu train. You only need to pay an extra of 410 yen one way.
If I were you, I would choose (B), but it's up to you.
By the way, an ordinary ticket (not the pass) from Tokyo area to Osaka area cost only 17,500 both ways including the Shinkansen express fee, and (long story short) with this ticket you can travel back and forth Kyoto if it's within 4 days. So unless you decide to travel longer, or unless you decide to travel further such as to Hiroshima, a 29,110 yen Japan Rail Pass doesn't really save you money.
All these things can be easier to understand if you could let a travel agent "draw/illustrate" it to you. But I hope this helps.