Once again I think you're putting too much faith in the modern scientific method. Just because something cannot be tested by our scientific instruments, which in the grand scheme of existence, may actually be quite crude, does not mean that it isn't so. Since you seem to be up to date on modern science you should be well aware that there exists occurrences in quantum theory, even in their own experiments, which the scientists still cannot explain. Even dark matter and energy, which you spoke of earlier, is more of a mystery to modern science than not.
We've attained a certain degree of scientific knowledge but to say that it encompasses all of existence is a naive assumption. It can be likened to those who, centuries ago, said that the world was flat, that the earth was the center of the universe and believed this without a doubt. With the scientific knowledge the individuals that believed this had, they felt this was the most logical conclusion they could make. How foolish do we think these ideas are now? I can envision a time in the future where the same view is held as to how we see things now.