me and my wife went for abt 2 weeks also, Free and Easy. I do agree if u include Hokkaido, it might be too rush.
We covered Tokyo(about 3 nights), Hakone(1 nights, near Tokyo), Lake Kawakuchiko(1 night), Osaka(2 nights), Mount Koya (1 night) Kyoto (4 nights). fight and everything add up to abt...