Tokyo-Mt.Fuji-Tokyo-Kyoto-Osaka

Hi Daniel, i really need your advice.pls help me .i will visit Japan on March 2014.here is my itinerary :

20th march = arrive at Haneda airport on 22.30pm.stay in tokyo.
21st march = tokyo (tsukiji,asakusa,shinjuku,akihabara)
22ndmarch= tokyo (shibuya)
23rdmarch = tokyo - gotemba - tokyo
24thmarch = tokyo - mt.fuji - tokyo (is it better if i go to mt.fuji and gotemba at the same day?)
25thmarch = tokyo - kyoto
26thmarch = kyoto - osaka
27thmarch = osaka
28thmarch = osaka-kansai airport (on 10 am)

my question are :
1.is it better for me to buy JR pass is or just normal ticket for 20thMarch until 28th March ?
2.i stay in mercure ginza tokyo (ginza itochome station).where is the closest JR station near my hotel?
3.from tokyo to gotemba and back to tokyo again....can i use JR pass to get there without spending extra money for buying buses or other train ticket?
4.from tokyo - Mt.fuji - tokyo (back to tokyo on the same day).....is it possible to get there without staying at mt.fuji area?how can i use JR pass to mt.fuji and try to saving money for buying other ticket as cheap as possible.i want to use jr pass more effectively and try not to have extra expenses for transportation.
5.when i arrive at haneda airport,and i want to activating my jr pass,where is the counter?and what time they are closing the ticket counter ? i am wooried that the jr pass counter already closed when i have exit from immigration checking at almost midnite.

Thanks !