On the way back from Australia (where I was for work) I went to Japan for 2.5 weeks of vacation. It was great! It was a bit hard at first with culture shock and the language barrier, but it is well organized so it is not that hard to find your way around. People are very friendly too, usually before I started wondering if I should ask somebody for directions I would be approached and asked if I needed any help (I guess it was obvious).
The first 2 weeks was organized by a travel agent in Amsterdam (Tozai). The first week they just booked the hotels in Tokyo and Kyoto and I figured out the rest. The second week was their Minshuku D tour, they booked japanese inns to stay in and the railpass. After the tour was done I realized that it was easy enough to travel around so I extended my stay for a couple of days and organized it myself. Early April is not too busy (it seemed) so it was easy to show up and find a place to stay.
Here is a google map with the places I visited.