Do we know where newly formed quark-antiquark pairs come from in the process of hadronization? The only explanations I have found are very vague, such as "spontaneously created from the vacuum" and because "it is more energetically favorable".
 A: It is not a vague explanation at all to say that they are created because it is energetically more favourable.
A hadronization interaction $q\bar q \to q q' \bar q \bar q'$ (or $q \to q q' \bar q'$, or something similar) is an allowed interaction in the underlying quantum field theory, that becomes ever more likely (its amplitude grows) as the energy scale of the process is raised. The "flux tubes" of the strong force field between two quarks hold a lot of energy (increasing linearly with distance in simple confinement models), and thus trying to seperate two quarks will, sooner or later, just create a new quark-antiquark pair. 
From where they come is not really a sensible question in this framework - it is an interaction not forbidden by any symmetry, so it can happen. Similarly, in collision experiments the energy scale is quite high anyway, leading to a burst of quarks even if there's no "attempted separation" of quarks going on (though you can also imagine it like that, since the high energy means that the quarks created in the collision will probably fly off very fast in more or less random directions)
A: They don't "come from" anywhere
in the sense that there is a reservoir of these thing sitting around waiting to be used.
Taken together the pair is equivalent to "nothing with some energy". So whenever you have that much energy and nothing, that combination can (not must or will, but might) simply become a quark-antiquark pair.
Equivalence here means "having all the same quantum numbers", and the idea that this is enough to allow things to transform from one type to another is one aspect of the "Totalitarian Principle" of quantum mechanics.
To emphasize: this is not something that can be understood by generalizing your intuitive picture of the world at human scales, it is a feature of the quantum world just as surprising as the results of a double-slit experiment.
A: Hadronization - the process by which colored objects form uncolored hadrons - is poorly understood, but we know the basics. Hadronization is a long-distance process, because, contrary to e.g. gravity, the strong force gets stronger at large distances.
When a quark-antiquark pair is created from a high-energy collision, they are always connected by a sort of "web" of gluons (the carriers of the strong force). Think of it as lots of strings connecting the two particles.
Some of the gluons connecting the pair might emit more gluons, and those gluons might decay into extra quark-antiquark pairs. The new quark-antiquark pairs ultimately form colorless hadrons with the original quarks. These hadrons are energetically favored, because the quarks bound into hadrons have a smaller mass than their free constituents. 
A: Here is a Feynman diagram of hadronization, i.e. parton showers

For this argument I am using the diagram  as input of  a quark antiquark pair from an incoming hadron interacting by  a gluon and scattering as an  off mass shell quark- antiquark.( in the figure the input is QED)
the curls are gluons, the light blue and purple and brown arrows are quarks.In this diagram, real particles, i.e. on mass shell, are  the jets on the right coming from the  paired quark-antiquarks. All the rest are within the interaction region and are virtual, off mass shell.
The answer in this context to the question:

Do we know where newly formed quark-antiquark pairs come from in the process of hadronization?

They come from the quark gluon sea within the interaction region. This link might help. Strong interactions make sure that quarks cannot become on mass shell in the lab. 

Fig. 3: A somewhat more accurate picture of a proton, filled with gluons (g) and quarks (u,d,s for up, down and strange) and antiquarks (same letters but with an overline bar.) These particles are whizzing around at speeds that are a significant fraction of the speed of light. The number of gluons and quark-antiquark pairs is enormously understated, for reasons of clarity. (If you look carefully, you'll see there are two more up quarks than up antiquarks, and one more down quark than down antiquark; that EXCESS of two up quarks and one down quark is what leads to the shorthand: "a proton is made from two up quarks and one down quark.")
Excess energy in proton proton scattering carried by the two scattered quarks in the first figure raise the energy of the virtual gluons and quark pairs in the sea, the energy ending up in jets of hadrons.The neutral in color pairs of quarks  and triplets  can take the energy away from the interaction region, being on mass shell.
