Using the Fourier expansion does work, though I have yet to completely evaluate every sum that makes up the overall integral. Recall the log-sine expansion,
$$\ln(\sin(x))=-\ln(2)-\sum_{k=1}^\infty \frac{\cos(2kx)}k$$
Expand the integrand as
$$x^2 \ln^2(2\cos(x)) = x^2 \bigg(\ln^2(2) + 2 \ln(2) \ln(\cos(x)) + \ln^2(\cos(x))\bigg)$$
Let
$$I_{m,n} = \int_0^{\frac\pi2} x^m \ln^n(\sin(x)) \, dx$$
so that
$$\begin{align*}
\mathcal I &= \int_0^{\frac\pi2} x^2 \ln^2(2\cos(x)) \, dx \\[1ex]
&= \ln^2(2) I_{2,0} + 2\ln(2) I_{2,1} + I_{2,2}
\end{align*}$$
$$\begin{align*}
I_{2,0} &= \int_0^{\frac\pi2} x^2 \, dx \\[1ex]
&= \frac{\pi^3}{24}
\end{align*}$$
$$\begin{align*}
I_{2,1} &= - \int_0^{\frac\pi2} \left(\frac\pi2-x\right)^2 \left(\ln(2) + \sum_{k=1}^\infty \frac{\cos(2kx)}k\right) \, dx \\[1ex]
&= -\frac{\pi^3}{24}\ln(2) - \sum_{k=1}^\infty \frac1k \int_0^{\frac\pi2} \left(\frac\pi2-x\right)^2 \cos(2kx) \, dx \\[1ex]
&= -\frac{\pi^3}{24}\ln(2) - \sum_{k=1}^\infty \frac1{2k} \int_0^\pi \left(\frac\pi2-\frac x2\right)^2 \cos(kx) \, dx \\[1ex]
&= -\frac{\pi^3}{24}\ln(2) - \sum_{k=1}^\infty \frac\pi{4k} \left(\frac{(-1)^k}{k^2} - \frac{-1+(-1)^k}{k^2}\right) \\[1ex]
&= -\frac{\pi^3}{24}\ln(2) - \frac\pi4 \zeta(3)
\end{align*}$$
$$\begin{align*}
I_{2,2} &= \int_0^{\frac\pi2} \left(\frac\pi2-x\right)^2 \left(-\ln(2)-\sum_{k=1}^\infty \frac{\cos(2kx)}k\right)^2 \, dx \\[1ex]
&= \int_0^{\frac\pi2} \left(\frac\pi2-x\right)^2 \left(\ln^2(2) + 2 \ln(2) \sum_{k=1}^\infty \frac{\cos(2kx)}k + \left(\sum_{k=1}^\infty \frac{\cos(2kx)}k\right)^2\right) \, dx \\[1ex]
&= \frac{\pi^3}{24}\ln^2(2) + \frac\pi4 \zeta(3) + \int_0^{\frac\pi2} \left(\frac\pi2-x\right)^2 \left(\sum_{k=1}^\infty \frac{\cos(2kx)}k\right)^2 \, dx \\[1ex]
&= \frac{\pi^3}{24}\ln^2(2) + \frac\pi4 \zeta(3) \\ &\qquad + \int_0^{\frac\pi2} \left(\frac\pi2-x\right)^2 \left(\sum_{k=1}^\infty \frac{\cos^2(2kx)}{k^2} + 2 \sum_{(k_1,k_2)\in\Bbb N^2} \frac{\cos(2k_1x)\cos(2k_2)x}{k_1k_2}\right) \, dx \\[1ex]
&= \frac{\pi^3}{24}\ln^2(2) + \frac\pi4 \zeta(3) + \sum_{k=1}^\infty \frac1{4k^2} \left(\frac{\pi^3}{12} + \frac\pi{8k^2}\right) \\ &\qquad + \frac\pi4 \sum_{(k_1,k_2)\in\Bbb N^2} \frac1{k_1k_2} \left(\frac1{(k_1+k_2)^2} + \frac1{(k_1-k_2)^2}\right) \\[1ex]
&= \frac{\pi^3}{24}\ln^2(2) + \frac\pi4 \zeta(3) + \frac{11\pi^5}{2880} \\&\qquad + \frac\pi4 \sum_{(k_1,k_2)\in\Bbb N^2} \frac1{k_1k_2} \left(\frac1{(k_1+k_2)^2} + \frac1{(k_1-k_2)^2}\right) \\[1ex]
&= \frac{\pi^3}{24}\ln^2(2) + \frac\pi8 \zeta(3) + \frac{3\pi^5}{320} \\&\qquad + \frac\pi4 \sum_{(k_1,k_2)\in\Bbb N^2} \frac1{k_1k_2} \frac1{(k_1-k_2)^2}
\end{align*}$$
where in the double sum, $k_1\neq k_2$.
To evaluate the first sum in $I_{2,2}$, I've used the same approach as shown here. Let
$$g(x) = \sum_{a=1}^\infty \sum_{b=1}^\infty \frac{x^{a+b}}{ab(a+b)^2}$$
Note that this includes the case of $a=b$. Differentiate and multiply by $x$ to recover $f$ (as in linked answer), integrate by parts to solve for $g$, and let $x\to1$ from below.
$$\begin{align*}
g'(x) &= \frac1x \int_0^x \frac{\ln^2(1-y)}y\,dy\\
&= \frac{\ln(x)\ln^2(1-x)+2\ln(1-x)\operatorname{Li}_2(1-x)-2\operatorname{Li}_3(1-x)}x
\end{align*}$$
Integrate by parts again to get
$$\begin{align*}
\sum_{(a,b)\in\Bbb N^2} \frac1{ab(a+b)^2} &= \int_0^1 \frac{\ln(x)\ln^2(1-x)+2\ln(1-x)\operatorname{Li}_2(1-x)-2\operatorname{Li}_3(1-x)}x\,dx \\
&= -\int_0^1 \frac{\ln(x)\ln^2(1-x)}x \, dx
\end{align*}$$
where IBP shows the last two integrals are absorbed into the first. Recalling the generating function for $H_n$ the harmonic numbers, $-\frac{\ln(1-x)}{1-x}$, it follows that
$$\sum_{(k_1,k_2)\in\Bbb N^2} \frac1{k_1k_3(k_1+k_2)^2} = \sum_{n=1}^\infty \frac{2H_n}{(n+1)^3} - \sum_{n=1}^\infty \frac1{2n^3} = \frac{\pi^4}{180} - \frac{\zeta(3)}2$$
in-progress
The second sum of $I_{2,2}$ still remains,
$$\sum_{(k_1,k_2)\in\Bbb N^2} \frac1{k_1k_2} \frac1{(k_1-k_2)^2}$$