Hi GundamWing,
This is the first time I hear of the word "moral" in mathematics... I won't be able to help you on that, but I can say something about square integrable functions (let's call all these functions L<sup>2</sup> from now on).
"Presumably the whole point of this argument is to show how a square integrable function (i.e., one whose Lebesgue integral converges) can be decomposed into a Fourier series, and by arguments of measure theory any arbitrary function can be described by simpler square-integrable functions defined over a complete complex inner-product space (Hilbert space). "
I won't go into detail of the proofs you mention here, but I can attempt to explain what it means.
First of all, you should know that all the maths you mention here are used in quantum mechanics. I will use that picture to make things clearer (hey, I am a physicist, not a mathematician, thus I am allowed to do that

).
You establish that any L<sup>2</sup> function can be decomposed in a Fourier series; this basically means that if you know a wavefunction W(x), then you can also calculate its associated momentum-function W'(p), which is simply the Fouriertransformed (closely related to Fourier series, as a matter of fact the L<sup>2</sup> functions are also Fourier-transformable). This is a mathematical formulation of the physical intuition: "If we know there is a particle with wavefunction W(x) then we also know it has some momentum that we can express in some function W'(p)".
Then you talk about Hilbertspaces and how any arbitrarily function can be expressed in L<sup>2</sup> functions. This is the first time I hear this result, but I'll assume it is correct. Then what does it mean ? Quite simple: if you take a function f(x), and you look at all (lineary independent) L<sup>2</sup>-functions q<sub>i</sub>(x), then you can find coefficients c<sub>i</sub> such that:
f(x) = <font face="symbol">S</font> c<sub>i</sub> q<sub>i</sub>(x)
up to any given precision (that is why you need a complete space, it eases the maths to express that "something is arbitrarily close to something else" or "up to any given precision they are the same"). The coefficients c<sub>i</sub> are defined as the inner product of f(x) and q<sub>i</sub>(x) in that Hilbertspace.
Compare this to ordinary vector calculus: you have three vectors (1,0,0) and (0,1,0) and (0,0,1) in which all the other vectors (a,b,c) can be expressed. Denote e<sub>i</sub> one of those three vectors, then:
(a,b,c) = <font face="symbol">S</font> c<sub>i</sub> e<sub>i</sub>
where the c<sub>i</sub> are a,b,c respectively (note by the way that c<sub>1</sub> a = scalar/inner product of (a,b,c) and e<sub>i</sub>(1,0,0), c<sub>2</sub> = scalar/inner product of (a,b,c) and e<sub>2</sub>, ... )
Hope this helps a bit,
Crisp