Short Answer
From the perspective of a scientific athiest, the natural sciences require very specific types of processes, reasoning, and evidence to validate the existence of beings. To start with the narrative of God and then conduct science to find explication and empirical results sufficient to explain that narrative has not gone well for even natural theologians historically, and as such God is simply a bad scientific theory. Of course, anyone with a religious epistemology would disagree simply because of different metaphysical presumptions including that God exists and is a universal cause. A scientist simply claims that such a presumption is an attempt to admit a claim without empirical evidence and against basic philosophical razors such Hitchen's razor. From WP:
"What can be asserted without evidence can also be dismissed without evidence."
You have decided to attack the theory of evolution indirectly, which is perhaps equal to atomic theory in significance and surety for scientists, but you do so with Aristotelian metaphysics (in the modern sense) which suffers from the deficiency of nearly 2,400 years of ignorance of history, philosophy, mathematics, and science. To reason about 21st-century scientific achievement and its philosophical implications with a philosophy conceived of in antiquity is bound to lead to problems. The failure of Aristotelian physics around 500 years ago obviously foreshadows the same short-comings in his argumentation.
Long Answer
You cover a lot of ground, but as an athiest, there's a difference in methodology between faith and skepticism, so two different metaphysical positions are at play. Science doesn't accept that which it cannot prove using one of the scientific methods. As such, in accordance with a proper understanding of materialism or physicalism, gods are at best an abstraction and have no physical embodiment to affect change. You seem to argue:
P0: Universal and particular causes exist.
P1: God exists and is a universal cause.
P2: Natural selection is a particular cause.
P3: Universal causes are ontologically prior to particular causes.
C: Natural selection cannot refute God's existence since God is required for natural selection.
A scientist just has a set of counterclaims to shift the burden of proof:
P'0: Universals and particulars are epiphenomenal, constructed, or non-existent.
P'1: One needs to use science to prove God's existence since he is not a brute fact.
P'2: Natural selection is a teleological biological definition and not an actual thing, and is ontologically prior to humans.
P'3: Mankind is ontologically prior to gods based on all the gods that have come and gone.
C': Therefore, according to physicalist, materialist, and empiricist thinking, atoms and their self-ordering are ontologically prior to humans which conceive of gods mistakenly from an evolutionary bias for agency detection.
Now here's the rub. What constitutes an informal fallacy is contextually driven, for a fallacy must be a persuasive inference that lacks adequate warrant and backing. And backings are often metaphysical presumptions (P0-P3 vs. P'1-P'3). So we are essentially dealing with aspects of the Agrippan Trilemma. How does one chose from various axioms? Science seems to suggest it's based on our feelings. From Antonio Demasio's Somatic Marker Hypothesis:
The somatic marker hypothesis, formulated by Antonio Damasio and associated researchers, proposes that emotional processes guide (or bias) behavior, particularly decision-making.1
"Somatic markers" are feelings in the body that are associated with emotions, such as the association of rapid heartbeat with anxiety or of nausea with disgust. According to the hypothesis, somatic markers strongly influence subsequent decision-making. Within the brain, somatic markers are thought to be processed in the ventromedial prefrontal cortex (VMPFC) and the amygdala.
Thus, believers believe because it feels good, and skeptics deny for the same reason.
