The main Shinkansen station at Shin-Osaka has a tourist information office which might be a good starting point when you arrive. It is quite easy to book some Japanese hotels online through english-speaking websites such as Hotelopia and Lastminute, but they give by no means the bigger picture of what's available. On the other hand, a good tourist office with some english spoken will hopefully be able to help you get booked into tradional ryokans and get you to the onsens around the Kyoto / Nara countryside. Strangely for a country with so much technology, there is not a lot of use of online booking and payments, so the smaller and Japanese-run places tend not to see many foreign bookings. Of course there will be specialist travel agents in the UK who'll book for you, at a price.
Hopefully you will be ordering your Japan rail pass to give you free travel on most systems (including the bullet trains) - order it through
http://www.seat61.com if you haven't done so yet, as you cannot buy a pass once you are inside Japan.
Osaka Castle - eat fried octopus teriyaki from stalls - great view from top of castle. Kyoto - the incredibly tranquil shrines in the parks - walk round Gion and see the Geishas. I stayed in the hotel Apa-Gion right on the corner of one of the parks and the Geisha district, lovely location and decent hotel. Nara - feral deer wander the streets cadging titbits - the great golden Buddha and temple, all within walking distance of railway station. Tokyo - where to start? It's an amazing place for just walking, riding the rail system and freelance gawping.
The one thing I didn't feel was done 'well' in Japan was the museums - and I speak as a museum lover. they are very dry line-ups of 'stuff' which you could sit at home and see online or read in a book if you wanted.
As 237 says, get a look at the guideboo