The problem with prayer.

[Neo-Scholastic]

To be clear, you do not subscribe to the notion of creation ex nihilo, then?

The structure of the argument is silent with respect to whether the physical universe always existed or whether it started at some hypothetical time 0. That said, Swedenborg did not subscribe to creation ex nihilo. His claimed that God created the universe “out of Himself”. This suggests a more neo-Platonic notion, similar to Plotinus.

1 On the quantum level, nothing from nothing isn't an accurate description of reality

It has been pointed out by many that a quantum vacuum isn’t exactly ‘nothing’ as traditionally understood. A proper atheistic response seems to be that a quantum vacuum adequately satisfied the role of necessary being. Perhaps. Deciding whether it can fill that role requires looking at additional criteria. Anything that is truly fundamental would also be non-contingent; it could not be other than how it is.
That does not seem to be the case with a quantum vacuum. A quantum vacuum follows specific physical laws that govern its capacities and behaviors. From where do these laws come? Either they are brute facts or they could have been otherwise. According to those laws (as I understand from others) the quantum vacuum is unstable. That instability means that it can exist in more than one state: productive or inert. That makes any change of state contingent some more fundamental cause. So presumably, it could be otherwise and whatever is truly fundamental must be found at a deeper level.

2 Assuming you are right, how did your classical "God" manage it - both for itself and for the Universe?

If there are absolutes, primitives, and/or fundamentals, then at some point those who wonder must accept some things as brute facts. The issue at hand is this: has the chain of explanations gone as deeply as possible? The Principle of Sufficient Reason only applies until it doesn’t. As a general rule, atheists stop too early and send boys to do the tasks of men. They take some things as brute facts, like quantum vacuum, even though those things do not satisfy the criteria for fundamentals.

3 What part(s) of the scriptural text lead inevitably to that conclusion to the exclusion of any other?

I’m not sure exactly what you mean by ‘that conclusion’. What conclusion? Anyway, we have strayed far from the OP topic of prayer.