This itinerary shows you the best of Japan, from Osaka to Aomori, passing by Kyoto, Nara, Mie, Nagoya, Fuji, Kamakura, Yokohama, Tokyo, and the north of Honshu for the festivals.
It's best done in july for the festivals, but it can be done anytime during the year as well. It also requires to rent a car in Japan for some less visited areas.
In the itinerary I put a lot of things to do everyday on purpose. You can decide to do everything if you wake up very early, or just go to your favourite ones in the list.
In term of transportation, I didn't use the JR pass this time, because it became too expensive and I rented a car to go off the beaten path to avoid the tourists crowds. I used IC card from my iPhone (super convenient), and google maps for every train, subway, and bus when I stayed in cities.
Overall budget for 30 days was around 5000 usd for 2 people, mainly because July is a very high season due to the many festivals, so cars and hotels were more expensive than usual. If you come in july (highly recommended though), book cars, hotels, festivals and other transports well in advance, at least 3-4 months.