travel to Japan

we have a plan to visit Japan on September 30 and come back from Osaka on October 9. 10 days 9 nights.
we have 5 people. would you give me suggestion for this trip. this is first time in Japan.
we will leaving on Sept. 30 arrive on October 1 at Haneda airport. ticket is not ready yet. So

1st day ( 10/01/13 ).... we don't know what time we will arrive , so we just look around at night in Tokyo first. stay first
night in Tokyo. 2nd day ( 10/02/13 ).....we will like to go ASAKUSA, SENSOJI, TOKYO MUSEUM (Edo), TOKYO NATIONAL
MUSEUM, GINZA, ROPPONGI , SHIBUYA, UENO PARK,.... Is it this places is very close to each other. should we take the JR Pass.... JR Pass is Shinkansen or subway?? because the trips is 10 days 9 nights so should I buy 10 days JR Pass in advance. JR Pass is have 7 days or 14 days only? so they sell 10 days JR pass also.

3rd day ( 10/03/13 )..... " " "

4th day ( 10/04/13 )..... We like to go YOKOHAMA ( we stay 4 nights at TOKYO)

5th day ( 10/05/13 ).... We like to go Hakone & Mt. Fuji, then on the way we can go to OSAKA and stay that
night in OSAKA.. 6th day (10/06/13 ) .... go to KYOTO ... visit Temple of the Golden Pavilion, Kiyomizu Temple, NIJO Castle,
Ryoanji Temple, Sanjusan gendo Hall and Silver Pavilion. I don't know all are close each other. how to arrange it ... at night I like to back to OSAKA. 7th day ( 10/07/13 ) .... go to NARA ....Nara Park, Todaiji Temple ,Daibutsu Buddha Status, Miho Asian Museum
give me advise...... 8th day ( 10/08/13 ).... go to KOBE..... Meriken Park Moto Machi Nankin Machi ???
9th day ( 10/09/13 )...... stay in OSAKA visit OSAKA places.
10th day 10/10/13 ) ..... back to LAX
I don't know how to arrange it and the place is very far or not.... how many places can we visit. all the places we can use JR pass or not ... what ticket I have to buy.... and where is good and reasonable hotel,.... we just stay to sleep ....