A continuation to your work:
$$\int_0^\infty\frac{x^2}{e^x-1}\ln\left(\frac{e^x}{e^x-1}\right)dx=\int_0^\infty\frac{x^2e^{-x}}{1-e^{-x}}\ln\left(\frac{1}{1-e^{-x}}\right)dx\\
\overset{e^{-x}=y}{=}-\int_0^1\frac{\ln^2y}{1-y}\ln(1-y)dy=\sum_{n=1}^\infty H_n\int_0^1 y^n \ln^2y dy\\=2\sum_{n=1}^\infty\frac{H_n}{(n+1)^3}=2\left(\sum_{n=1}^\infty\frac{H_n}{n^3}-\sum_{n=1}^\infty \frac1{n^4}\right)\\=2\left(\frac54\zeta(4)-\zeta(4)\right)\\=\frac12\zeta(4)$$
The result $\sum_{n=1}^\infty \frac{H_n}{n^3}=\frac54\zeta(4)$ follows from using the Euler identity:
$$\sum_{n=1}^\infty \frac{H_n}{n^q}= \left(1+\frac{q}{2} \right)\zeta(q+1)-\frac{1}{2}\sum_{k=1}^{q-2}\zeta(k+1)\zeta(q-k)$$
In our calculations, I used the following identities:
$$\sum_{n=1}^\infty H_n x^n=-\frac{\ln(1-x)}{1-x}$$
$$\int_0^1 x^{n-1}\ln^axdx=\frac{(-1)^a a!}{n^{a+1}}$$
Addendum:
The integral $\int_0^1 \frac{\ln^2x}{1-x}\ln(1-x)dx$ can be evaluated without using Euler identity, the first way is by using beta function and the second way is by using the rule
$$\int_0^1\frac{x^{n}\ln^m(x)\ln(1-x)}{1-x}\ dx=\frac12\frac{\partial^m}{\partial n^m}\left(H_n^2+H_n^{(2)}\right)$$
Just set $m=2$ then let $n$ approach $0$ we get
$$\int_0^1 \frac{\ln^2x}{1-x}\ln(1-x)dx=\frac12\frac{\partial^2}{\partial n^2}\left(H_n^2+H_n^{(2)}\right)_{n\to 0}\\=\frac12\left(4H_nH_n^{(3)}+2\left(H_n^{(2)}\right)^2+6H_n^{(4)}-4\zeta(2)H_n^{(2)}-4\zeta(3)H_n-\zeta(4)\right)_{n\to 0}\\=-\frac12\zeta(4)$$