I'm not able to follow the steps for your PDE, but I can at least provide an over-the-top alternative.
Note that the integral converges for $0 <|y| < x$. Using $\displaystyle \ln\left(1+f(x\right))=\int_{0}^{1}\frac{f(x)}{1+tf(x)}dt$ and Fubini's Theorem, we have
$$
\begin{align}
I &:= \int_{0}^{\pi}\ln\left(x+y\cos t\right)dt \\
&= \int_{0}^{\pi}\ln xdt+\int_{0}^{\pi}\ln\left(1+\frac{y}{x}\cos t\right)dt \\
&= \pi\ln x+\int_{0}^{\pi}\int_{0}^{1}\frac{\frac{y}{x}\cos t}{1+\frac{uy}{x}\cos t}dudt \\
&= \pi\ln x+\frac{y}{x}\int_{0}^{1}\int_{0}^{\pi}\frac{\cos t}{1+\frac{uy}{x}\cos t}dtdu \\
&= \pi\ln x+\frac{y}{2}\int_{0}^{1}\int_{0}^{2\pi}\frac{\cos t}{x+uy\cos t}dtdu \\
&= \pi\ln x+\frac{y}{2}\int_{0}^{1}\int_{0}^{2\pi}\frac{e^{2it}+1}{2x+uy\left(e^{2it}+1\right)}dtdu. \\
\end{align}
$$
Parameterize $z = e^{it}$ on the unit circle $C$ centered at the origin, going counterclockwise with a radius of $1$. Then $I$ becomes
$$\pi\ln x+\frac{y}{2}\int_{0}^{1}\oint_{C}^{}\frac{1+z^{2}}{2xz+uy\left(1+z^{2}\right)}\frac{dz}{iz}du = \pi\ln x+\frac{y}{2i}\int_{0}^{1}\oint_{C}^{}\frac{1+z^{2}}{2xz^{2}+uyz\left(1+z^{2}\right)}dzdu.$$
The simple poles of the integrand are $z_0 :=0$, $z_1 := \displaystyle \frac{\sqrt{x^{2}-y^{2}u^{2}}-x}{uy}$, and $z_2 := \displaystyle \frac{-\sqrt{x^{2}-y^{2}u^{2}}-x}{uy}.$ Notice that $z_0$ and $z_1$ are always inside $C$ but not $z_2$. Using the residues at the simple poles, the double integral becomes
$$
\begin{align}
&\int_0^1 2\pi i \left(\operatorname{Res}\left(\frac{1+z^{2}}{2xz^{2}+uyz\left(1+z^{2}\right)}, z = z_1\right) + \operatorname{Res}\left(\frac{1+z^{2}}{2xz^{2}+uyz\left(1+z^{2}\right)}, z = z_2\right)\right)du \\
=& \int_0^1 2\pi i \left( \lim_{z \to z_0} (z-z_0) \cdot \frac{1+z^{2}}{2xz^{2}+uyz\left(1+z^{2}\right)} + \lim_{z \to z_1} (z-z_1) \cdot \frac{1+z^{2}}{2xz^{2}+uyz\left(1+z^{2}\right)}\right)du. \\
\end{align}
$$
We proceed as follows:
$$
\begin{align}
I &= \pi\ln x+\pi y\int_{0}^{1}\left(\frac{1}{uy}-\frac{x}{uy\sqrt{x^{2}-u^{2}y^{2}}}\right)du \\
&= \pi\ln x+\pi\int_{0}^{1}\frac{\sqrt{x^{2}-y^{2}u^{2}}-x}{u\sqrt{x^{2}-y^{2}u^{2}}}du \\
&= \pi\ln x-\pi\int_{x}^{\sqrt{x^{2}+y^{2}}}\frac{v-x}{\sqrt{x^{2}-v^{2}}\frac{v}{y}}\frac{v}{y\sqrt{x^{2}-v^{2}}}dv \\
&= \pi\ln x+\pi\int_{x}^{\sqrt{x^{2}+y^{2}}}\frac{dv}{x+v} \\
&= \pi\ln x\ +\ \pi\Big[\ln\left(x+v\right)\Big]_{x}^{\sqrt{x^{2}+y^{2}}} \\
&= \pi\ln\left(\frac{x+\sqrt{x^{2}-y^{2}}}{2}\right). \\
\end{align}
$$