Hi Sam,
It's actually very useful that you write a good amount of what you would like, don't want and don't know about. It also gives me a bit of an idea of what kind of a person you may be. Japan is perfect for just traveling on the go without a completely planned itinerary. It's actually something I love to do, just get on the train and sort things once you arrive somewhere. Japan is absolutely perfect when it comes to this, every station has a tourist information and you can ask them for help with accommodations. Just say your budget and they will call all the hotels/hostels/etc in the area until they find a place for you. This is also one of the most amazing things of the JR Pass, you can just can get on the train whenever you feel like it.
Okay, now that I have a little more information let's try to fill in your itinerary a little more.
After Tokyo, why not visit Fuji? Fuji is best reached from Tokyo anyway and some fresh mountain air will be good after a week of city life. From there you could head to Hakone, this is a very beautiful area, with onsen, traditional inns and many interesting spots. Although early in your trip a good tip for shopping in the area are the Gotemba Premium Outlets. The view of Fuji is also amazing in Hakone.
After Hakone I would suggest going down to Kansai / Takayama, this is the area where Kyoto, Osaka, Nara and Kobe are located. Kansai offers enough to keep you busy for days. In Kyoto I would advise a visit to Kyomizudera temple, I've always found this as one of the most impressive sights in Kyoto. You can also view the entire city from there.
As for the JR Pass, I would suggest a 21 day JR Pass to use when you start travel to Kansai, from there you should be able to use it to cover all your train travel. Once it expires head to Okinawa and fly back to Tokyo. This would work out very well in terms of routing.
Note that I had written most of above already before I got your 3rd post but I still think it all applies. Now for some feedback on your itinerary. Going to Okinawa is great! I would recommend taking the ferry from Kagoshima to Okinawa, it is possible to make a stop on the islands in between and making the ferry trip is an amazing experience. Then from Okinawa, just fly back to Tokyo.
Also love the visit to Takayama but I would recommend staying maybe a night longer and make a visit to Shirakawago. Before travelling to Kyoto why not make a stop at Kanazawa. Kanazawa has beautiful castle, one of the most beautiful gardens in Japan (called Kenryoku-en) and the local geisha quarter is as authentic as it gets (it's better than Kyoto's).
Lastly Nara is a great visit as well but you will be able to see it within a day so one day is enough. It is also within 1h travel from Kyoto or Osaka and is best visited as a day trip.
I guess that covers most of what I had to say for now :) Let me know if I can help with anything!
Daniel