Ah! The JR pass is full and good for a week in May, but perhaps I can extend that. Thank you all very much. I will definitely add these places to where to go. But, where are Nara, Himeji, and Atami?
So if I go from Tokyo to Nikko/Kamakura, then to Nagoya, next kyoto, then Osaka, and finally down to Hiroshima, Fukoaka, and Nagasaki - then how long would it take to get to these areas or near these areas with the JR railway or other ways of transportation?
I'm sorry this is a bit clustered right now, I really need to even this out and perhaps spend a little more time to check things out in different places. I'd love to see Kagoshima and Kochi somehwere in there. Perhaps I need two weeks to check out all of these places? Thank you all for your help so far, I hope this is not too much to ask.