If we consider again the formula
\begin{align}\int^1_0\frac{\mathrm{Li}_{p-1}(x) \mathrm{Li}_q(x) \log(1-x)}{x}\, dx+\int^1_0\frac{\mathrm{Li}_p(x) \mathrm{Li}_{q-1}(x) \log(1-x)}{x}\, dx &= \sum_{m=2}^{q-1}(-1)^{m-1} \zeta(q-m+1) S_{p,m} \\&+ (-1)^{q-1} \sum_{k\geq 1} \frac{H_k^{(p)} H_k}{k^q}-\mathscr{H}(p,q)\\& +\zeta(q) \zeta(p+1)-\zeta(q)\mathscr{H}(p-1,1) \end{align}
Then letting $$p=2,q=3$$ yields
$$-\int^1_0\frac{ \mathrm{Li}_3(x) \log^2(1-x)}{x}\, dx+\int^1_0\frac{\mathrm{Li}_2(x)^2 \log(1-x)}{x}\, dx = -\zeta(2) S_{2,2} + \sum_{k\geq 1} \frac{H_k^{(2)} H_k}{k^3}-\mathscr{H}(2,3)+ \zeta^2(3)-\zeta(3) \mathscr{H}(1,1)$$
Hence we have
$$\sum_{k\geq 1} \frac{H_k^{(2)} H_k}{k^3} = -\int^1_0\frac{ \mathrm{Li}_3(x) \log^2(1-x)}{x}\, dx+\zeta(2) S_{2,2} + \mathscr{H}(2,3)-\zeta^2(3)+\zeta(3) \mathscr{H}(1,1)+\frac{\zeta(2)^3}{3}$$
Now we use that
$$\int^1_0\frac{ \mathrm{Li}_3(x) \log^2(1-x)}{x}\, dx=\frac{97}{12} \zeta(6)-\zeta^2(3)-\zeta^3(2)$$
$$S_{2,2}=\frac{7}{4}\zeta(4)$$
$$\mathscr{H}(2,3)=\frac{\zeta(3)^2}{2}$$
$$\mathscr{H}(1,1)=2\zeta(3)$$
So we have the interesting result
$$\sum_{k\geq 1} \frac{H_k^{(2)} H_k}{k^3} =- \frac{97}{12} \zeta(6)+\frac{7}{4}\zeta(4)\zeta(2) + \frac{5}{2}\zeta(3)^2+\frac{2}{3}\zeta(2)^3$$