I will be travelling from Miami to Japan(landing NRT) for about three weeks(leave 8/12/12 return 9/2/12). I am having a difficult time planning bits of an itinerary and would really appreciate any help/advice/recommendations etc. I lived in Osaka, Japan for a year as an exchange student back on 2007, so I have some idea of what's going on but would still really like some advice. This time I would like to see all the things I didn't know about, or couldn't get to the last time around. Reading some of the posts on here I came to realize just how little I actually saw outside of Tokyo and Kansai region while I was there.
Also, I will be travelling with a friend(1st time to Japan) and we would both really like to see some nice nature spots so I am trying to include trips to Mt Fuji and Yakushima. I understand this might be an ambitious undertaking but we would like to try if possible. In regards to Yakushima, I know portions of the trip are not included with the JR pass, does anyone have any idea how much it costs to get there? Roughly?
Another thing I need to find is a good car factory with English tours for my friend to visit but have no idea what is a good place to go to or where to fit it in my itinerary. Also, I would be interested in visiting some nice hot springs if possible, but don't know too much about where to go. If someone could suggest possible options for these things I would be much obliged.
I think we will be getting a 2 week JR pass because I have read they are somewhat useless within Tokyo but please correct me if I'm wrong. Here is a very rough, tentative itinerary, please feel free to rearrange/omit/add anything you think beneficial:
12-Aug LEAVE MIAMI
13-Aug ARRIVE TOKYO
15-Aug HIROSHIMA/MIYAJIMA - Activate 2 week JR pass to get here
21-Aug NARA/MOUNT KOYA
22-Aug MOUNT KOYA/OSAKA
2-Sep LEAVE TOKYO
3-Sep ARRIVE MIAMI