Let us integrate along the contour $\Gamma$, which is the semicircle of radius $R$ described above. Let $C_R$ be the arc of the contour with radius $R$. We may say that
$$\oint_{\Gamma}\frac{\cos z}{z^2+a^2}\, dz=\int_{-R}^{R}\frac{\cos x}{x^2+a^2}\, dx+\int_{C_R}\frac{\cos z}{z^2+a^2}\, dz$$
Note that $\cos x = \operatorname{Re}\,(e^{ix})$. Thus
$$
f(z)=\frac{\operatorname{Re}\,(e^{iz})}{z^2+a^2} = \operatorname{Re}\,\left(\frac{e^{iz}}{(z+ia)(z-ia)}\right)
$$
Because $f(z)$ can be written ias $g(z)e^{iaz}$ and suffices all of the conditions of Jordan's lemma, we see that the integral along the arc tends to zero when $R\to \infty$. Thus
$$
\lim_{R\to\infty}\oint_{\Gamma}\frac{\cos z}{z^2+a^2}\, dz=\lim_{R\to\infty}
\int_{-R}^{R}\frac{\cos x}{x^2+a^2}\, dx+0
$$
To solve the LHS, we find the residues. The residue, similar to the one you found is
$$
b=\frac{e^{i^2a}}{ia+ia}=\frac{e^{-a}}{2ia}
$$
Thus
$$
\displaystyle\int_{-\infty}^{\infty} \frac{\cos x}{x^{2} + a^{2}}\, dx=
\lim_{R\to\infty}\oint_{\Gamma}\frac{\cos z}{z^2+a^2}\, dz=\operatorname{Re}\,\left(\displaystyle\int_{-\infty}^{\infty} \frac{e^{iz}}{z^{2} + a^{2}}\, dz\right)
=\operatorname{Re}\,(2\pi ib)=\operatorname{Re}\,(2\pi i\frac{e^{-a}}{2ia}) = \frac{\pi e^{-a}}{a}
$$
Similarly, with $\displaystyle\int_{-\infty}^{\infty} \frac{x \sin x}{x^{2} + a^{2}}\ dx$ we change $\sin x$ to $\operatorname{Im}\,(e^{ix})$ and make the function complex-valued.
$$g(z)=\frac{z\sin z}{z^2+a^2}=\operatorname{Im}\,\left(\frac{ze^{iz}}{(z+ia)(z-ia)}\right)$$
Jordan's lemma again can be used to show that the integral around the arc tends to zero as $R\to\infty$. We then proceed to find the residues.
The residue of pole $z_1=ia$ is
$$b=\frac{iae^{-a}}{2ia}=\frac{e^{-a}}{2}$$
$z_1$ is the unique pole in the contour, so upon multiplying its residue, $b$, with $2\pi i$ we find:
$$
\displaystyle\int_{-\infty}^{\infty} \frac{x \sin x}{x^{2} + a^{2}}\, dx=
\lim_{R\to\infty}\oint_{\Gamma} \frac{x \sin x}{x^{2} + a^{2}}\, dz=
\operatorname{Im}\,\left(\displaystyle\int_{-\infty}^{\infty} \frac{ze^{iz}}{(z+ia)(z-ia)}\, dz\right)=
\operatorname{Im}\,(2\pi ib)=
\operatorname{Im}\,(2\pi i \frac{e^{-a}}{2})=
\operatorname{Im}\,(\pi e^{-a}i)=
\pi e^{-a}
$$