Otro enfoque
Utilizando la misma estrategia de @omegadot,
de este artículo página $105$ tenemos
$$\overline{H}_n=\ln2-\int_0^1\frac{(-x)^n}{1+x}\ dx$$
multiplicamos ambos lados por $\frac{(-1)^nH_n}{n^2}$ luego $\sum_{n=1}^\infty$ obtenemos
$$S=\ln2\sum_{n=1}^\infty\frac{(-1)^nH_n}{n^2}-\underbrace{\int_0^1\frac{1}{1+x}\sum_{n=1}^\infty\frac{H_nx^n}{n^2}\ dx}_{\large \mathcal{I}}\tag1$$
De aquí tenemos
$$\sum_{n=1}^\infty\frac{H_{n}}{n^2}x^{n}=\operatorname{Li}_3(x)-\operatorname{Li}_3(1-x)+\ln(1-x)\operatorname{Li}_2(1-x)+\frac12\ln x\ln^2(1-x)+\zeta(3)$$
$$\Longrightarrow \mathcal{I}=\underbrace{\int_0^1\frac{\operatorname{Li}_3(x)}{1+x}\ dx}_{\large \mathcal{I}_1}-\underbrace{\int_0^1\frac{\operatorname{Li}_3(1-x)}{1+x}\ dx}_{\large \mathcal{I}_2}+\underbrace{\int_0^1\frac{\ln(1-x)\operatorname{Li}_2(1-x)}{1+x}\ dx}_{\large \mathcal{I}_3}$$ $$+\underbrace{\frac12\int_0^1\frac{\ln x\ln^2(1-x)}{1+x}\ dx}_{\large \mathcal{I}_4}+\zeta(3)\underbrace{\int_0^1\frac{1}{1+x}\ dx}_{\ln2}$$
$$\mathcal{I}_1=\int_0^1\frac{\operatorname{Li}_3(x)}{1+x}\ dx=-\sum_{n=1}^\infty(-1)^n\int_0^1 x^{n-1}\operatorname{Li}_3(x)\ dx$$ $$=-\sum_{n=1}^\infty(-1)^n\left(\frac{\zeta(3)}{n}-\frac{\zeta(2)}{n^2}+\frac{H_n}{n^3}\right)$$
$$=\ln2\zeta(3)-\frac54\zeta(4)-\sum_{n=1}^\infty\frac{(-1)^nH_n}{n^3}$$
$$\mathcal{I}_2=\int_0^1\frac{\operatorname{Li}_3(1-x)}{1+x}\ dx\overset{1-x\to x}{=}\int_0^1\frac{\operatorname{Li}_3(x)}{2-x}\ dx$$ $$=\sum_{n=1}^\infty\frac1{2^n}\int_0^1 x^{n-1}\operatorname{Li}_3(x)\ dx =\sum_{n=1}^\infty\frac1{2^n}\left(\frac{\zeta(3)}{n}-\frac{\zeta(2)}{n^2}+\frac{H_n}{n^3}\right)$$
$$=\ln2\zeta(3)-\zeta(2)\operatorname{Li}_2\left(\frac12\right)+\sum_{n=1}^\infty\frac{H_n}{2^nn^3}$$
$$\mathcal{I}_3=\int_0^1\frac{\ln(1-x)\operatorname{Li}_2(1-x)}{1+x}\ dx\overset{1-x\to x}{=}\int_0^1\frac{\ln x\operatorname{Li}_2(x)}{2-x}\ dx$$
$$=\sum_{n=1}^\infty\frac1{2^n}\int_0^1 x^{n-1}\ln x\operatorname{Li}_2(x) \ dx=\sum_{n=1}^\infty\frac1{2^n}\left(\frac{2H_n}{n^3}+\frac{H_n^{(2)}}{n^2}-\frac{2\zeta(2)}{n^2}\right)$$
$$=2\sum_{n=1}^\infty\frac{H_n}{2^nn^3}+\sum_{n=1}^\infty\frac{H_n^{(2)}}{2^nn^2}-2\zeta(2)\operatorname{Li}_2\left(\frac12\right)$$
$$\mathcal{I}_4=\frac12\int_0^1\frac{\ln x\ln^2(1-x)}{1+x}\ dx\overset{1-x\to x}{=}\frac12\int_0^1\frac{\ln(1-x)\ln^2x}{2-x}\ dx$$
$$=\frac12\sum_{n=1}^\infty\frac1{2^n}\int_0^1 x^{n-1}\ln(1-x)\ln^2x \ dx$$ $$=\frac12\sum_{n=1}^\infty\frac1{2^n}\left(\frac{2\zeta(3)}{n}+\frac{2\zeta(2)}{n^2}-\frac{2H_n}{n^3}-\frac{2H_n^{(2)}}{n^2}-\frac{2H_n^{(3)}}{n}\right)$$
$$=\ln2\zeta(3)+\zeta(2)\operatorname{Li}_2\left(\frac12\right)-\sum_{n=1}^\infty\frac{H_n}{2^nn^3}-\sum_{n=1}^\infty\frac{H_n^{(2)}}{2^nn^2}-\sum_{n=1}^\infty\frac{H_n^{(3)}}{2^nn}$$
Combinando los resultados de $\mathcal{I}_1$, $\mathcal{I}_2$, $\mathcal{I}_3$ y $\mathcal{I}_4$
$$\Longrightarrow \mathcal{I}=2\ln2\zeta(3)-\frac54\zeta(4)-\sum_{n=1}^\infty\frac{(-1)^nH_n}{n^3}-\sum_{n=1}^\infty\frac{H_n^{(3)}}{2^nn}$$
ahora enchufa este resultado en $(1)$
$$ \Longrightarrow S=\frac54\zeta(4)-2\ln2\zeta(3)+\ln2\sum_{n=1}^\infty\frac{(-1)^nH_n}{n^2}+\sum_{n=1}^\infty\frac{H_n^{(3)}}{2^nn}+\sum_{n=1}^\infty\frac{(-1)^nH_n}{n^3}$$
Finalmente, sustituye
$$\sum_{n=1}^\infty\frac{(-1)^nH_n}{n^2}=-\frac58\zeta(3)\tag{i}$$
$$\sum_{n=1}^\infty\frac{H_n^{(3)}}{2^nn}=\operatorname{Li}_4\left(\frac12\right)-\frac{5}{16}\zeta(4)+\frac78\ln2\zeta(3)-\frac14\ln^22\zeta(2)+\frac1{24}\ln^42\tag{ii}$$
$$\sum_{n=1}^\infty\frac{(-1)^nH_n}{n^3}=2\operatorname{Li}_4\left(\frac12\right)-\frac{11}{4}\zeta(4)+\frac74\ln2\zeta(3)-\frac12\ln^22\zeta(2)+\frac1{12}\ln^42\tag{iii}$$
obtenemos
$$S=3\operatorname{Li}_4\left(\frac12\right)-\frac{29}{16}\zeta(4)-\frac34\ln^22\zeta(2)+\frac18\ln^42$$
Nota que los resultados de $(i)$ y $(ii)$ se obtienen usando las funciones generadoras
$$\sum_{n=1}^\infty\frac{H_{n}}{n^2}x^{n}=\operatorname{Li}_3(x)-\operatorname{Li}_3(1-x)+\ln(1-x)\operatorname{Li}_2(1-x)+\frac12\ln x\ln^2(1-x)+\zeta(3)$$
$$\sum_{n=1}^\infty \frac{H_n^{(3)}}{n}x^n=\operatorname{Li}_4(x)-\ln(1-x)\operatorname{Li}_3(x)-\frac12\operatorname{Li}_2^2(x).$$
Respecto a $(iii)$, ya está calculado aquí.
Lo interesante de este enfoque es que algunas series complicadas se cancelaron y solo usamos resultados bien conocidos de la serie armónica.