You wrote: "First, human intelligence took the raw materials and, assembled the technology and substance needed to make X-rays. Second, although unseen, all the particles necessary to complete this process and make it repeatable have remained organized and consistent so as to make the application of human intelligence possible. "
Reply:
You seem to have an odd view. Is it your view that X-rays did not exist before Roentgen discovered them?
I cannot fathom what you mean by 'organized matter'. A snow crystal is highly organized. A mammalian blasosphere in utero is highly organized and develops into a fetus, seemingly contrary to the 2nd law. X-rays and gamma rays are evident in the universe beyond earth. I do not understand your point.
I thought by "X-rays" you meant the medical application. Either type of X-ray is designed, intelligible, useful, and behaves according to predictable laws. Either can comfortably be considered a product of intelligent design and thus further studied by science.