Oh, I was confused by the way you presented the numbers. So, what you mean is the height of one story should be 6ft instead of 10ft. When you said 6ft*6ft I thought you were talking about the layout as seen from top.
Anyway. By looking at different coasters I came to the conclusion that the height of one story varies between 6ft and 10ft. From above the bentposts form a square of 10ft*10ft (just like they do with the woodbuilder. So, the only thing that sometimes might be wrong is the height of one story. However, I think it's good that they are at 10ft (like many real coasters too, mind you) as to reduce the overall amount of supports and therefor guarantee higher fps.
The dimensions of the wooden beams themselfs is about correct.
Buster.