Hi Colleen,
In order for a 7 day JR Pass to be worth buying, you need to plan to spend at least ¥28,300 on travel. Looking at your itinerary as it stands I think you'll be better off buying separate tickets - I don't think there is any way to cut your trip right now so that it becomes cost effective to use a JR Pass.
Firstly, the travel from Kansai Airport and between Tennoji and Kyoto is relatively cheap, so you would not need a rail pass for the first 5 days of your trip:
- Kansai airport > Tennoji: ¥2470, (33mins, 46km)
- Tennoji > Kyoto: ¥3570, (52mins, 53km)
TOTAL: ¥6040 for 2 legs
This leaves the remaining 7 days of travel from day 5 onwards:
- Kyoto > Takayama: ¥9980, (193mins, 314km)
- Takayama > Tokyo: ¥14600, (273mins, 532km)
- Tokyo > Hamamatsucho: ¥150, (6mins, 3km)
- Hamamatsucho > Haneda airport international terminal: ¥150, (6mins, 3km)
TOTAL: ¥24880 for 4 legs
As you can see, while expensive, this travel does not amount to more than the ¥28,300 cost of the 7 day rail pass.
In order for a 7 day rail pass to be worthwhile, you'll need to plan on doing another ¥3420 on travel. We have some posts on day trips from Tokyo with a JR Pass that will easily tip you over this, but it very much depends on personal preference.
Regarding your other questions:
In the Hypedia I notice we have to pay a Fare as well as seat Fee(reserved and unreserved seat). How does that work?
In Japan there is a basic fare on all JR trains. In addition to this there is a seat fee issued on special trains (such as bullet trains and other super express services). The seat fee depends on the class of seat you choose to use and is a component part of the full fare.
which JR train should I take that are cover in the Rail pass.
We have a blog post and video on using Hyperdia for Japan Rail Pass holders that will let you find trains that are suitable for a JR Pass. In general however, it is all trains and buses except the Nozomi and Mizuho class bullet trains. All other bullet trains are accessible.
Hope this helps!