Hello!
Glad to hear that arrangements have been made for your account!
Japan has Holiday Inns, too, especially in Tokyo and Osaka, and there is a wide range of accommodations for tourists, starting from cheap places for backpackers and Japanese inns of all kinds to moderately priced Western-style hotels and top hotels.
In all cases, the rooms are generally clean, and private rooms are usually available.
I don't know what price range you have in mind and will recommend starting out at a moderately priced, reputable hotel for the first couple of days in Japan. I think books like Lonely Planet and Fodor (I think there is one for Japan) should provide such info. After that, you'll find how things are in Japan and will be able to act on your own!
Outside the major cities, you can stay at "minshuku" (Japanese inns that are actually private homes converted to provide accommodations for toursts), which are cheap.
Considering that you can afford it, I recommend splurging once in a while at a premier spa resort to indulge yourself in fine Japanese dining and hot spring bathing in scenic landscape.
Wait for Nagashima-san to come up with extensive info on the Web!