Train and buses schedules

Hi!I am going to Japan next Tuesday and have some "last minute" questions.
I am trying to figure out timetables of trains and buses to "lose" as little time as possible (we'll be in a tight schedule), but I am finding a bit difficult and confusing - i.e. not sure if my Japan Rail Pass is valid or not, and Hypedia gives some weird results. In case the rail pass is not valid, has anyone got suggestion of the cheapest route?
The plan is (for 3 weeks):
Narita-Tokyo
Tokyo-Kamakura
Tokyo-Fujiyoshida (to climb Mt. Fuji)
5th station-Kawaguchiko
Kawaguchiko-Kyoto
Kyoto-Nara
Osaka (overnight when coming from Nara)-Koyasan
Koyasan-Miyajima Island
Miyajima-Himeji castle-Higashiura (Awaji Island)
Higashiura-Takayama
Takayama-Kamikochi
Kamikochi-(Matsumoto?)-Tokyo

Main doubts are:
-Tokyo-Fujiyoshida - We are climbing all Fuji-san from the shrine on sat. 11/8, so we'd like to get there as early as possible. My cousin will be waiting for us on the 5th station. And we are staying in a hut on the 8th station.
How can I find times? And how do I book seats?
-5th station Kawaguchiko - will the bus service be frequent? is it better to book a seat in advance? we will be taking this one on sunday 12/8 morning, so I suppose lots of people will be descending at the same time.
-Kawaguchiko to Kyoto - bus to Mishima station and then JR. which company to book seats? (approximate time? i asked that in a previous post, but I can't find it...sorry!)
-osaka-koyasan - is the nankai-dentesu line the cheapest? i read it's 1230 yen including the cable car, no JR.
-Miyajima island to Higashiura (Awaji Island)
-We are spending a couple of days in the Alps. Takayama and Kamikochi. From Kamikochi we are heading back to Tokyo, but I read Matsumoto is on the way. Do you think it's worth stopping over? Also, which transport is better (more scenic)? bus or train?

Thank you very much in advance. I asked some of these questions some weeks ago, but I can't find that post...

I am really looking forward to this trip!

I think this is the other thread:
http://www.japan-guide.com/forum/quereadisplay.html?0+37578

thanks Uji. That's great!

hello i be like to ask how much is the time traveling from Nakahara-ku to Tokyo station with train? because i will need be about 8;10 am at tokyo station, if i start in 7 am are will be good?