I’d write it mostly the way you wrote it since that appears to be what the numbers say. I would change this sentence
Is the assumption “that humans share common ancestry with apes,” even strictly necessary to determine your numbers since you are comparing diversity in humans with the rate of mutation in humans? Even if it was a part of the calculations of some of the research which you drew data from, I see it as superfluous and a potential distraction from your actual findings. I don’t see where it is essential that your team assume that in order to get the numbers that you did.
Regarding the phrase “God has not intervened with physical miracles” I think I would be way more specific. Something like “We assume God has not intervened in a super-natural way so as to give a false appearance of age to the genetic data.” I think your results are going to be dismissed as based on invalid assumptions by those who believe in miracles unless you phrase it in such a way that you are only assuming He won’t do any miracles which are outside His character.
The only thing else I might suggest, and maybe this is the next study and not this one, is that you address the idea that a flood wiped out all Y-chromosomes except for one sometime long after Adam. If your MRCA for just Y-chromosomes also shows a date in the distant past, it might be worthwhile to point that out. There is not just the question of the nature of Adam to consider, but the flood and Noah as well.