[Firebird]

Just some quick answers/suggestions:
As said many times, its ok to get around in Tokyo with english, but every bit Japanese will be helpfull.
Mt Fuji: I have stayed in Fujiyoshida and there was a nice Youth Hostel were the owner speaks a little bit English and you get a private Tatami room, its not a Ryokan, but its ok.
Nikko: The staff in Nikko Tourist Information speaks English, so you should be fine in things like accomodation (you might want to book ahead if you are in high season). Otherwise Nikko is easy to navigate without knowing Japanese.
Matsushima Bay: Defenetly a very nice place and well worth visiting. With Sendai only 40 minutes away, you might want to spend the night in Sendai. Otherwise is also quite easy to navigate, some english signes and many restaurants have english menu (try Gyutan wich is cow toung).

I havent been to Hakone, Kyoto, Miyami Iland and Dewa Sanzan, but the last seems a little bit more remote. I will probably stay there in a few days, so ill let you know about getting around.