What exactly are "primordial fluctuations"? Are "primordial fluctuations" essentially the same as "virtual particles" and "quantum fluctuations" that created the universe from nothing like what is featured in the Lawrence Krauss book, A Universe from Nothing?
 A: I haven't read Krauss' book, but it seems the "quantum fluctuations" referred to is something invoked to explain the origin of the Universe itself; i.e. why is there something rather than nothing.
This is not what the term "primordial fluctuations" refers to. Although this is also quantum fluctuations, in the sense that their origin is described by quantum mechanics, their existence assumes the existence of a Universe in the first place. Quantum mechanics' uncertainty principle implies that the Universe — however it came into existence and not really considering the cause — was clumpy on very small scales. When the Universe was $10^{-36}$–$10^{-33}$ seconds old, during the epoch called inflation, these clumps grew in size to cosmological sizes, later collapsing under the force of gravity to the structures we see today as clusters, galaxies, and stars.
A: It's well-known, that the large-scale structure is incredibly rich. Although on the largest cosmological scales the Universe looks boring (isotropic and homogeneous), at slightly smaller scales that are still very large (we're talking about considering clusters of galaxies as a single entity), we see incredibly rich structure, of filaments, walls and voids, like a sponge, e.g. https://kicp.uchicago.edu/research/highlights/images/highlight-060611-3.jpg. 
In the early universe, there was no structure, only a hot plasma. The radiation pressure from photons etc. prevents gravity from condensing other non-relativistic particles. This `washing out' of structure means that if we assume only normal matter contributes to gravity, we cannot dynamically generate the observed rich sponge-like structure we see at the large-scale today.
In order to see the amount of structure in the Universe, we need dark matter. But even that is not enough. In addition to the dark matter, we need `seeds' of gravitational potential wells to speed up the gravitational condensation of dark matter.
The seeds are called `primordial fluctuations' and occur before the existence of a hot thermal plasma, in the very early universe. In inflationary cosmology, it's proposed that the quantum fluctuations provide the seeds for structure. Inflation enlarges to the quantum fluctuations, causing them to become classical and form the seeds necessary for large-scale structure.
