I know that if a matrix $\mathbf{A}$ is orthogonal, then $x\cdot x = \mathbf{A}x\cdot \mathbf{A}x$ because $\mathbf{A}x\cdot \mathbf{A}x = (\mathbf{A}x)^T \mathbf{A}x = x^T\mathbf{A}^T\mathbf{A}x=x^T\mathbf{A}^{-1}\mathbf{A}x=x^Tx=x\cdot x$.
If the inner product over functions is chosen to be, $$ f\cdot g = \int_{-\infty}^{\infty} f(x)\overline{g(x)} \,\mathrm{dx} $$
Then it seems intuitive to me that if I normalize the Fourier transform the right way, then it will act like it's "orthonormal," and preserve this inner product so that $\mathcal{F}[f]\cdot \mathcal{F}[g] = f\cdot g$. How do I prove this, and which normalization should I use to make it true?
You are looking for the Plancherel theorem. A part of it states that the Fourier transform preserves the inner product in $\mathscr{L}^2$.
The result is that, $$ \int_{-\infty}^\infty f(x)\overline{g(x)} \, dx = \int_{-\infty}^\infty \widehat{f}(\xi) \overline{\widehat{g}(\xi)} \, d\xi $$ When both $f$ and $g$ are in $\mathscr{L}^2$.