Choosing JR Pass for travel

Hi,
I have to planned to travel Japan from 24 March 2014 as follow:
Day 1 - arrive Osaka 24th March 2014
Day 2 - Go to Fukuoka
Day 3 - Go to Hiroshima - Miyajima - return to Fukuoka
Day 4- Fukouka region
Day 5- Fukouka region- to Nagasaki
Day 6 - Return to Osaka
Day 7 - Osaka -Kobe- Osaka
Day 8- Osaka -Kyoto
Day 9 - Kyoto site seeing
Day 10- Kyoto , Nara and region-Kyoto
Day 11 - Kyoto and surroundings
Day 12- Kyoto - Mt. Fuji
Day 13- Mt. Fuji
Day 14- Return to Osaka
Day 15- Osaka
Day 16 - Osaka to Malaysia ( 7th April 2014)

How do I select my JR Pass, sounds a bit complicated.
Can you please recommend where to stay to Kyoto, We want to stay in Ryokan in Mt. Fuji, hopefully convenient
with Onsen.
Your help is appreciated, thank you.
Gilbert Goh