Actually I trained with the high school team that Daniel, as well as some other future world-class runners, ran for when he first came to Japan.
I think there are several reasons why the Japanese do so well.
1. Body type - The average Japanese is small of stature and the perfect build for a distance runner. When I first came to Japan and I was fit and looked about like the average Japanese except I was taller.
2. Marathon runners are respected and compensated for their efforts. The top runners are famous in Japan, are often seen in commercialls and are supported be major corporations.
3. Japanese don't have many other sports where they can be competitive on the world stage so a lot of effort is put into making them successful in this arena.
If you are a successful runner in Japan the rewards are great, fame, money etc. It is the same as being a successful baseball/football player in the states. If there is a possibility of making this dream happen there are many motivating reasons to do everything to make it happen.
From my experience teaching at high schools and universities in Japan I have found that the average Japanese isn't any more disciplined than the average American they just have more physically suited people to choose from and more reasons to be successful at it