Rewriting
Use the trigonometric identity $\csc^2(x) = \cot^2+1$. Rewrite the integral as
$$\int\limits_{\alpha}^{\beta}\csc^2(x)\left(-\frac{\log\cot x}{\cot^2+1}\right)\,\mathrm{d}x$$
After substituting $u=\cot x$ we get the integral
$$-\int\limits_{\cot(\alpha)}^{\cot(\beta)}\frac{\log u}{u^2+1}\,\mathrm{d}u=-\left[\frac{i}{2}\int\limits_{\cot(\alpha)}^{\cot(\beta)}\frac{\log u}{u+i}\,\mathrm{d}u-\frac{i}{2}\int\limits_{\cot(\alpha)}^{\cot(\beta)}\frac{\log u}{u-i}\,\mathrm{d}u\right].$$
First integral
Sub $v=u+i$. You should get
$$\int\limits_{\cot(\alpha)+i}^{\cot(\beta)+i}\frac{\log v-i}{v}\,\mathrm{d}v = \int\limits_{\cot(\alpha)+i}^{\cot(\beta)+i}\frac{\log iv+1}{v}\,\mathrm{d}v+\log(-i)\int\limits_{\cot(\alpha)+i}^{\cot(\beta)+i}\frac{1}{v}\,\mathrm{d}v.$$
Integral 1
Sub $w=-iv$. This will get us to
$$-\int\limits_{1-i\cot(\alpha)}^{1-i\cot(\beta)}-\frac{\log 1-w}{w}\,\mathrm{d}w = -\Big[\operatorname{Li}_2(1-i\cot(\beta))-\operatorname{Li}_2(1-i\cot(\alpha))\Big]$$
Integral 2
Note that $\log(-i)=-i\pi/2$. We get:
$$-i\pi/2\Bigg[\log(\cot(\beta)+i)-\log(\cot(\alpha)+i)\Bigg].$$
Second Integral
Sub $v=u-i$. You should get
$$\int\limits_{\cot(\alpha)-i}^{\cot(\beta)-i}\frac{\log v+i}{v}\,\mathrm{d}v = \int\limits_{\cot(\alpha)-i}^{\cot(\beta)-i}\frac{\log 1-iv}{v}\,\mathrm{d}v+\log(i)\int\limits_{\cot(\alpha)-i}^{\cot(\beta)-i}\frac{1}{v}\,\mathrm{d}v.$$
Integral 1
Sub $w=iv$. This will get us to
$$-\int\limits_{i\cot(\alpha)-1}^{i\cot(\beta)-1}-\frac{\log 1-w}{w}\,\mathrm{d}w = -\Big[\operatorname{Li}_2(i\cot(\beta)-1)-\operatorname{Li}_2(i\cot(\alpha)-1)\Big]$$
Integral 2
Note that $\log(i)=i\pi/2$. We get:
$$i\pi/2\Bigg[\log(\cot(\beta)-i)-\log(\cot(\alpha)-i)\Bigg].$$
Values for $\alpha$ and $\beta$
For the first orignal integral we have
$$-\frac{{\pi}\left(\log\left(\tan^2\left(\frac{7{\pi}}{36}\right)+1\right)-\log\left(\tan^2\left(\frac{5{\pi}}{36}\right)+1\right)\right)+{i}\left(2\operatorname{Li}_2\left({i}\tan\left(\frac{7{\pi}}{36}\right)+1\right)-2\operatorname{Li}_2\left(1-{i}\tan\left(\frac{7{\pi}}{36}\right)\right)-2\operatorname{Li}_2\left({i}\tan\left(\frac{5{\pi}}{36}\right)+1\right)+2\operatorname{Li}_2\left(1-{i}\tan\left(\frac{5{\pi}}{36}\right)\right)\right)}{4}$$
For the second orignal integral we have
$$-\dfrac{{\pi}\left(\log\left(\tan^2\left(\frac{{\pi}}{12}\right)+1\right)-\log\left(\tan^2\left(\frac{{\pi}}{36}\right)+1\right)\right)+{i}\left(2\operatorname{Li}_2\left({i}\tan\left(\frac{{\pi}}{12}\right)+1\right)-2\operatorname{Li}_2\left(1-{i}\tan\left(\frac{{\pi}}{12}\right)\right)-2\operatorname{Li}_2\left({i}\tan\left(\frac{{\pi}}{36}\right)+1\right)+2\operatorname{Li}_2\left(1-{i}\tan\left(\frac{{\pi}}{36}\right)\right)\right)}{4}$$
A few last words
I added these values numerically and I got the right result. The integral is solved but it still needs some long (algebraic) operations to prove the end result. But the Polylogarithm $\operatorname{Li}_2$ looks promising. Maybe I will add the final derivation later on, but first I have to take a break of this monster challenge.
Also, if someone finds a faster way and all of this is useless I would be twice as happy. Nonetheless I hope it has helped you at least a bit.