"...But surely the Schrodinger's equation doesn't apply to the Fourier coefficients, right?"
To begin, I have to say that I personally always found to the word "quantization" as very confusing and not exactly explanatory as to what kind of action it refers to.
Now coming to your question that I copied above, the answer is in fact yes you can (sort of). The thing that you should be aware of is that the very term "quantization" is in fact a hail from the heroic early days of Quantum Theory when people like Niels Bohr where doing things noting short of wizardry (Correspondence Principle, Complementarity Principle, etc) to somehow squeeze the Physics they grew up with into the Procrustean bed of the contemporary experimental evidence.
It is then that the protocol for the "quantization of a theory" has crystallized. In short, the algorithm was/is as follows:
- Formulate your problem in classical terms as a Hamiltonian theory just the way Goldstein, Landau&Lifshits vol.1, or any other Classical Mechanics textbook of your liking, prescribes. Namely, you have to find:
1-1) a set of (classical) variables $\{ Q_i \}$ that fully describe your system. These variables dubbed "generalized coordinates" do not necessarily have to look like "coordinates". They can be anything but the necessary requirement is that knowing them you should always be able to tell how your system looks like $\textit{now}$. For example the $3N$ coordinates of $N$ particles or any other (linearly independent) linear combination of them (hence the "generalized" quality of the generalized coordinates).
1-2) Construct the corresponding classical Lagrangian in terms of generalized coordinates $\{ Q_i \}$ and their time derivatives ("generalized speeds") $\{ \dot{Q}_i \}$.
1-3) Using the found Lagrangian $L(\{ Q_i \}, \{ \dot{Q}_i \})$ find "generalized momenta" $\{ P_i\}$ according to $P_i \equiv \frac{\partial L}{\partial \dot{Q}_i}$.
This was all classical so far. Here comes the magic of "quantization":
- Up till now all $Q_i$'a and $P_i$'s were nothing but a bunch of number. Now you say that you forgo that, and say you have no idea anymore as to what they are. The only thing you $\textit{postulate}$ you know is that
$$Q_i P_j - P_j Q_i = i\hbar \delta_{ij}$$
This is called Heisenberg commutation relations and this is the central element, the keystone of Quantum Theory. To dispell any possible misunderstanding, regardless of how Heisenberg arrived at them, they do not follow from anywhere. Quite in contrary, everything follows from it.
- This is the last and the hardest step. You have to $\textit{guess}$ what ever could those $Q_i$'a and $P_i$'s be. For example, Mr. Born had an idea that they could be matrices. Why not? Matrices don't commute, hence the Heisenberg commutation relations are satisfied. By consistently following this $\textit{representation}$, Heisenberg has constructed his Matrix Mechanics.
Schoedinger (or rather Dirac) went another way and noticed that Heisenberg commutation can be obtained if one thinks of $P$'s and $Q$'s as some sort of calculus operation performed of continuous functions. Hence Schoedinger's Wave Mechanics (you can try to find your own representation if you want, with some other algebraic objects. Who knows, maybe it will open new vistas in Physics, as Feynman's approach did).
To summarize you can quantize anything. Just make sure this something is part of a set of variables describing the state of of the system on the classical level, and that you can find "momenta" corresponding to this something. Once you have them, just postulate the Heisenberg commutation relation between them and find a suitable representation.
P.S. When I say "anything", I really mean anything. Take the predator-prey (Lotka-Volterra) equation. The "coordinates" would be the species' populations. The corresponding dynamics can be formulated in terms of a Hamiltonian (e.g. https://www.math.tecnico.ulisboa.pt/~rfern/Meus-papers/HTML/equadiff.pdf), then you can "quantize" it too. How useful it is? Probably not at all. But my point was that Fourier components are not the most absurd objects to quantize at all.
$\textbf{EDIT}$: Q: "...why should the Fourier coefficients satisfying the same equations as decoupled harmonic oscillators lead to the same quantization?" A: Since you are free to choose objects for $Q_i$ and $P_i$ as long as they commute according to Heisenberg, it is often convenient to "steal" them from another problem someone has solved before. Solutions don't smell. If two systems have equivalent Hamiltonians, so do their spectra.