For technical reasons it is easier to find the Fourier cosine series of $\log^2\left(2\cos x\right)$ first.
By squaring and applying formal manipulations
$$\begin{eqnarray*} \log^2\left(2\cos x\right) &=& \sum_{j,k\geq 1}\frac{(-1)^{j+k}}{jk}\cos(2jx)\cos(2kx)\\ &=& \frac{1}{2}\sum_{j,k\geq 1}\frac{(-1)^{j+k}}{jk}\left[\cos(2(j+k)x)+\cos(2|j-k|x)\right]\\&=&\frac{1}{2}\sum_{j\geq 1}\frac{\cos(2j x)+1}{j^2}+\sum_{j\geq 1}\sum_{d\geq 1}\frac{(-1)^d}{j(j+d)}\left[\cos(2(2j+d)x)+\cos(2dx)\right]\\&=&\frac{\pi^2}{12}+\sum_{m\geq 1}c_m \cos(2mx)\end{eqnarray*}$$
where the coefficient $c_m$ equals:
$$ c_m = \frac{1}{2m^2}+\sum_{j\geq 1}\frac{(-1)^m}{j(j+m)}+\sum_{1\leq j<\frac{m}{2}}\frac{(-1)^m}{j(m-j)}$$
and by partial fraction decomposition this coefficient is related with the harmonic numbers.
For instance:
$$\sum_{j\geq 1}\frac{1}{j(j+m)} = \frac{H_{m-1}}{m}.$$
I guess you may take it from here.