Japan is BIG!
So don't do it all at one trip if you really want to see all of Japan.
It might be better to split Japan into several areas, then visit each area or few areas in each visit to Japan that you will do a couple of times. It might be best to allocated at least a month or two for each area.
Japan could be divided into several areas:
Hokkaido island
East Honshu island
Central Honshu island
West Honshu island
Shikoku island
Kyushu island
Okinawa islands
Interestingly, when the J.N.R. company was splitted up into the JR companies, it was divided roughly that way, with the exception of Okinawa, considering that when J.N.R. was divided there were no railways in Okinawa and only recently the Yui monorail was open to service in Okinawa.
Anyway, Central Honshu might be the first place to start.
There are several routes one can go.
Central Honshu -> East Honshu -> Hokkaido
Central honshu -> Shikoku -> West Honshu -> Part of Kyushu or the whole Kyushu if you prefer
Central Japan -> West Honshu -> Kyushu
As for Okinawa. It might be better to visit Taiwan first, then catch a ferry to Okinawa from there. Okinawa was so far away from Japan that it might better to consider it as another country.
As for rail pass. Considering on how long you stay in Japan, it might be better to disregard the Japan Rail Pass that covered the operations of the JR companies for the entire Japan. It might be better to get regional passes (even non JR ones) or get the Seishun 18 Kippu pass (that are regulary used by travelers with low budget).
As matter in fact, it might be better to get passes that you can use non consecutively (like the Seishun 18 Kippu or the JR East's 4 days flexi pass) or passes that has a short valid time (like a day pass or a three days pass)