Many, many items to discuss here, but let me respond in brief:
***Intelligent design means that the universe behaves in accordance with known or unknown "laws". For example, Einstein's General Relativity would be such a law. However, it is known that this theory does not apply to the microscopic world.***
How do you define laws? Your paper mentions fundamental symmetries as a causative agent to quantum laws, etc, however why is that a symmetry law is not a 'law'? What breaks symmetries - a symmetry breaking law?
***If the universe were intelligently designed according to Laws such as the laws of classical physics, then such laws or other similar laws should also apply to microscopic physics.***
Classical laws are (or might be) an approximation of other laws that apply microscopic physics. This more fundamental set of laws might be an approximation of something even more fundamental and so on. Theism is the belief that the fundamental axioms of the universe is that God exists, what is your belief on the fundamental axioms?
***What is the nature of these similar laws? Well, if a number of systems are identical and have identical initial conditions, then classical laws would deem that they behave exactly the same. If the microscopic laws are similar, or if they are of intelligent design, then we should expect exact behavor from identical systems.***
Not necessarily. "Intelligent design" might be a pattern that the universe conforms to that even inhibits the behavior of microscopic systems in an approximate fashion and not an exact non-fuzzy fashion.
***However, on the microscopic scale, what we measure is that identical atoms, excited to the same state at the same time, will not decay at the same time. The decay time is probablistic. The laws of probability apply, which are based in large measure on randumbness, not intelligence.***
I don't see how probablistic behavior is ruled out by an intelligent designed universed, and, for that matter, I don't see how a random 'originating' universe is supported by probablistic behavior seen in the universe. Laws of probability are based on the truth of certain mathematical axioms, but this only begs the question. Why are those axioms true? Are they randomly true (i.e., brute fact), or are they true because God exists?
***This does not imply the lack of a gods, or gods, or even the supernatural- just a lack of intelligent design. Perhaps the god(s) are learning from us as we discover more and more about the universe. The behavior of gods recorded in human history would be evident of such a case.***
I don't see much substance to your argument against some kind of intelligent design to the universe. It seems your paper is mainly focused on providing a probablistic account for quantum theories, from that point of departure you make some rather broad statements that are not so well argued.