Unless you really, really like snow or want to go skiing at one of Hokkaido resorts, stay away from Hokkaido in January. Especially if you're Australian and have just come from Hong Kong and have never experienced temperatures far below freezing.

Also, forget actually going to Mt. Fuji in the winter. You can't climb it at that time of year (well, you probably could, illegally, but it would be bitterly cold and possibly snowy). At that time of year, when the air tends to be dry, the mountain that the English-speaking foreign students at my university called "the Fooj" is often visible from tall buildings in Tokyo and/or the north side of the Shinkansen from Tokyo to Kyoto. It's visible for a good long time, too.

It sounds as if you'll do enough traveling for a JR Pass, but whether to get a 7-day or 14-day pass depends on...how long you plan to stay.

By the way, you should definitely get a guide book and do a search on some of the previous posts here.