We make use of the identity
$$ \sum_{n=-\infty}^{\infty} \frac{1}{a^{2} - (x + n\pi)^{2}} = \frac{\cot(x+a) - \cot(x-a)}{2a}, \quad a > 0 \text{ and } x \in \Bbb{R}. $$
Then for $\alpha, \beta > 0$ it follows that
\begin{align*}
I := \mathrm{PV}\int_{0}^{\infty} \frac{\log\cos^{2}(\alpha x)}{\beta^{2} - x^{2}}
&= \frac{1}{2} \mathrm{PV} \int_{-\infty}^{\infty} \frac{\log\cos^{2}(\alpha x)}{\beta^{2} - x^{2}} \, dx \\
&= \frac{\alpha}{2} \mathrm{PV} \int_{-\infty}^{\infty} \frac{\log\cos^{2}x}{(\alpha\beta)^{2} - x^{2}} \, dx \\
&= \frac{\alpha}{2} \sum_{n=-\infty}^{\infty} \mathrm{PV} \int_{-\frac{\pi}{2}}^{\frac{\pi}{2}} \frac{\log\cos^{2}x}{(\alpha\beta)^{2} - (x+n\pi)^{2}} \, dx \\
&= \frac{\alpha}{2} \mathrm{PV} \int_{-\frac{\pi}{2}}^{\frac{\pi}{2}} \left( \sum_{n=-\infty}^{\infty} \frac{1}{(\alpha\beta)^{2} - (x+n\pi)^{2}} \right) \log\cos^{2}x \, dx \\
&= \frac{1}{4\beta} \mathrm{PV} \int_{-\frac{\pi}{2}}^{\frac{\pi}{2}} (\cot(x+\alpha\beta) - \cot(x-\alpha\beta)) \log\cos^{2}x \, dx,
\end{align*}
where interchanging the order of integration and summation is justified by Tonelli's theorem applied to the summation over large indices $n$. Then
\begin{align*}
I
&= \frac{1}{4\beta} \mathrm{PV} \int_{-\frac{\pi}{2}}^{\frac{\pi}{2}} (\cot(x+\alpha\beta) - \cot(x-\alpha\beta)) \log\cos^{2}x \, dx \\
&= \frac{1}{2\beta} \mathrm{PV} \int_{-\frac{\pi}{2}}^{\frac{\pi}{2}} (\cot(x+\alpha\beta) - \cot(x-\alpha\beta)) \log\left|2\cos x\right| \, dx \tag{1}
\end{align*}
Here, we exploited the following identity to derive (1).
$$ \mathrm{PV} \int_{-\frac{\pi}{2}}^{\frac{\pi}{2}} \cot(x+a) \, dx = 0 \quad \forall a \in \Bbb{R}. $$
Now with the substitution $z = e^{2ix}$ and $\omega = e^{2i\alpha\beta}$, it follows that
\begin{align*}
I
&= \frac{1}{2\beta} \Re \mathrm{PV} \int_{|z|=1} \left( \frac{\bar{\omega}}{z - \bar{\omega}} - \frac{\omega}{z - \omega} \right) \log(1 + z) \, \frac{dz}{z}. \tag{2}
\end{align*}
Now consider the following unit circular contour $C$ with two $\epsilon$-indents $\gamma_{\omega,\epsilon}$ and $\gamma_{\bar{\omega},\epsilon}$.
Then the integrand of (2)
$$ f(z) = \left( \frac{\bar{\omega}}{z - \bar{\omega}} - \frac{\omega}{z - \omega} \right) \frac{\log(1 + z)}{z} $$
is holomorphic inside $C$ (since the only possible singularity at $z = 0$ is removable) and has only logarithmic singularity at $z = -1$. So we have
$$ \oint_{C} f(z) \, dz = 0. $$
This shows that
\begin{align*}
I
&= \frac{1}{2\beta} \Re \lim_{\epsilon \downarrow 0} \left( \int_{-\gamma_{\omega,\epsilon}} f(z) \, dz + \int_{-\gamma_{\bar{\omega},\epsilon}} f(z) \, dz \right) \\
&= \frac{1}{2\beta} \Re \left( \pi i \mathrm{Res}_{z=\omega} f(z) + \pi i \mathrm{Res}_{z=\bar{\omega}} f(z) \right) \\
&= \frac{1}{2\beta} \Re \left( - \pi i \log(1 + \omega) + \pi i \log(1 + \bar{\omega}) \right) \\
&= \frac{\pi}{\beta} \arg(1 + \omega)
= \frac{\pi}{\beta} \arctan(\tan (\alpha \beta)).
\end{align*}
In particular, if $\alpha\beta < \frac{\pi}{2}$ then we have
$$ I = \pi \alpha. $$
But due to the periodicity of $\arg$ function, this function draws a scaled saw-tooth function for $\alpha > 0$. Of course, $I$ is an even function of both $\alpha$ and $\beta$, so the final result is obtained by even extension of this saw-tooth function.
Best Answer
You can also directly apply Dirichlet's test (the integral of the numerator is zero when taken over a period, therefore uniformly bounded on all finite intervals).
We have $$\cos^{2 k} u = 2^{-2 k} \binom {2 k} k + 2^{1 - 2 k} \sum_{1 \leq j \leq k} \binom {2 k} {k - j} \cos 2 j u, \\ \sum_{k \geq 0} \frac {(i \alpha \cos u)^{2 k}} {(2 k)!} = J_0(\alpha) + \sum_{j \geq 1} \sum_{k \geq j} 2^{1 - 2 k} \binom {2 k} {k - j} \frac {(i \alpha)^{2 k}} {(2 k)!} \cos 2 j u = \\ J_0(\alpha) + 2 \sum_{j \geq 1} (-1)^j J_{2 j}(\alpha) \cos 2 j u.$$ Doing the same calculation for odd indices and integrating termwise, we obtain $$I(\beta, j) = \int_0^\infty \frac {\cos j u} {1 + \beta u} du = \frac {\left( \frac \pi 2 - \operatorname{Si}(\omega) \right) \sin \omega - \operatorname{Ci}(\omega) \cos \omega} \beta, \quad \omega = \frac j \beta, \\ F(\alpha, \beta) = 2 \sum_{j \geq 1} i^j J_j(\alpha) I(\beta, j).$$ $J_j(\alpha)$ decays superexponentially for a fixed $\alpha$ (roughly speaking, it oscillates when $j < \alpha$ and then decays rapidly).