In the EL equation I use the following colored-labels
$$
\color{blue}{\frac{\partial}{\partial x^\mu}}\color{red}{\left(\frac{\partial \mathcal{L}}{\partial (\partial_\mu \phi)}\right)} - \color{orange}{\frac{\partial \mathcal{L}}{\partial \phi}} = 0
$$
$\mathcal{L} = \mathcal{L}_{\rm KG}^{\rm free}$
For the Lagrangian
$$
\mathcal{L}_{\rm KG}^{\rm free} = \frac{1}{2}\partial_\nu\phi\partial^\mu\phi - \frac{1}{2}m^2\phi^2
$$
we can calculate
- $\color{orange}{\rm orange}$:
$$
\color{orange}{\frac{\partial \mathcal{L}}{\partial \phi}} = -m^2\phi
$$
- $\color{red}{\rm red}$:
\begin{eqnarray}
\color{red}{\frac{\partial \mathcal{L}}{\partial (\partial_\mu\phi)}} &=& \frac{1}{2}\frac{\partial }{\partial (\partial_\mu\phi)}(\partial_\nu \phi \partial^\nu\phi) = \frac{1}{2}\eta^{\nu\alpha}\frac{\partial }{\partial (\partial_\mu\phi)}(\partial_\nu \phi\partial_\alpha \phi) \\
&=& \frac{1}{2}\eta^{\nu\alpha}(\delta^\mu_\nu \partial_\alpha\phi + \partial_\nu\phi\delta^\mu_\alpha) = \frac{1}{2}\eta^{\mu\alpha} \partial_\alpha\phi + \frac{1}{2}\eta^{\nu\mu}\partial_\nu\phi \\
&=& \frac{1}{2}\eta^{\mu\nu}\partial_\nu\phi +\frac{1}{2}\eta^{\mu\nu}\partial_\nu\phi \\
&=& \eta^{\mu\nu}\partial_\nu\phi = \partial^\mu\phi
\end{eqnarray}
- $\color{blue}{\rm blue}$:
\begin{eqnarray}
\color{blue}{\frac{\partial}{\partial x^\mu}}\color{red}{\left(\frac{\partial \mathcal{L}}{\partial (\partial_\mu \phi)}\right)} &=& \partial_\mu\partial^\mu \phi = \eta^{\mu\nu}\partial_\mu\partial_\nu\phi \\
&=& \underbrace{\eta^{00}}_{1}\partial_0\partial_0\phi + \underbrace{\eta^{i0}}_{0}\partial_i\partial_0 \phi + \underbrace{\eta^{0i}}_{0}\partial_i\partial_j \phi +
\underbrace{\eta^{ij}}_{-\delta^{ij}}\partial_i\partial_j \phi \\
&=& \ddot{\phi} - \nabla^2\phi
\end{eqnarray}
The signs on this last expression may be different for you, depending on your choice of the metric. Putting everything together
$$
\ddot{\phi} - \nabla^2\phi + m^2\phi = 0
$$
$\mathcal{L} = \mathcal{L}_{\rm EM}$
In this case the Lagrangian is
$$
\mathcal{L}_{\rm EM} = -\frac{1}{4}(\partial^\alpha A^\beta - \partial^\beta A^\alpha)(\partial_\alpha A_\beta - \partial_\beta A_\alpha) - j^\alpha A_\alpha
$$
and
- $\color{orange}{\rm orange}$:
$$
\color{orange}{\frac{\partial \mathcal{L}}{\partial A_\nu}} = j^\alpha\delta^\nu_\alpha = j^\nu
$$
- $\color{red}{\rm red}$:
\begin{eqnarray}
\color{red}{\frac{\partial \mathcal{L}}{\partial (\partial_\mu A_\nu)}} &=&
-\frac{1}{4}\frac{\partial}{\partial (\partial_\mu A_\nu)}(\partial^\alpha A^\beta - \partial^\beta A^\alpha)(\partial_\alpha A_\beta - \partial_\beta A_\alpha) \\
&=&-\frac{1}{4}\frac{\partial}{\partial (\partial_\mu A_\nu)}(\eta^{\alpha\sigma}\eta^{\beta\rho}\partial_\sigma A_\rho - \eta^{\beta\rho}\eta^{\alpha\sigma}\partial_\rho A_\sigma)(\partial_\alpha A_\beta - \partial_\beta A_\alpha) \\
&=& -\frac{\eta^{\alpha\sigma}\eta^{\beta\rho}}{4}\frac{\partial}{\partial (\partial_\mu A_\nu)}
(\partial_\sigma A_\rho - \partial_\rho A_\sigma)
(\partial_\alpha A_\beta - \partial_\beta A_\alpha) \\
&=&-\frac{\eta^{\alpha\sigma}\eta^{\beta\rho}}{4}\frac{\partial}{\partial (\partial_\mu A_\nu)}
(\partial_\sigma A_\rho \partial_\alpha A_\beta + \cdots) \\
&=&-\frac{\eta^{\alpha\sigma}\eta^{\beta\rho}}{4} (\delta^{\mu}_{\sigma}\delta^{\nu}_{\rho}\partial_\alpha A_\beta + \partial_\sigma A_\rho\delta^{\mu}_{\alpha}\delta^{\nu}_{\beta} + \cdots) \\
&=&-\frac{1}{4}(\eta^{\alpha\mu}\eta^{\beta\nu}\partial_\alpha A_\beta + \eta^{\mu\sigma}\eta^{\nu\rho}\partial_\sigma A_\rho + \cdots )
\end{eqnarray}
I will leave the rest for you