If you want to save money, you should probably avoid the "speed trains" (Shinkansen) and stick to buses and local trains. They are slower, but also less expensive, and it sounds to me like you have more time than money, so the trade might be worth it.
Also, getting to Okinawa would require either a domestic plane or a long ferry ride, so unless you have some pressing need to see it, stick to the 4 main islands of Japan.
These are tons of posts here discussing itineraries, look up some of them for ideas, and buy a good Japanese guidebook (I like Lonely Planet)
Amazon.com: Japan (Country Guide): Chris Rowthorn: Books This will give you a lot of places to visit, and how to get there (with plenty of maps), as well as places to stay. I always carried my Lonely Planet guide with me when traveling in Japan.
As for a rough itinerary suggestion, how about (in order) Tokyo, Nikko, Matsumoto, Kamikochi, Takayama, Kanazawa, Kyoto, Nara, Osaka, Mt Koya, Himeji, Hiroshima, Miyajima, Fukuoka, Nagasaki, Matsuyama and Shikoku, Nagoya, Hakone, Yokohama, and back to Tokyo. It's a long looping trip over 3 of Japan's main islands, but you have a month or 2 there, right? You could see all that in about 25-30 days minimum, and you'd experience a vast cross-section of Japan, new and old, urban cities and the rural countryside, and all the main sights.