Admittedly the derivation in the lecture was quite terse,
So it may have been hard to follow.
The lecture makes this approach for a plane EM wave travelling in $+z$ direction
$$\vec{E}(z,t)=E_o\hat{x}\cos(kz-\omega t) \tag{1}$$
$$\vec{B}(z,t)=B_o\hat{y}\cos(kz-\omega t) \tag{2}$$
with some constants ($E_0,B_0,k,\omega$).
Like every EM field this EM wave needs to satisfy the Ampere-Maxwell law
$$\oint\vec{B}\cdot d\vec{l} =
\mu_0\epsilon_0\frac{d}{dt}\underbrace{\int\vec{E}\cdot d\vec{A}}_{\Phi_E}. \tag{3}$$
We can use this law to deduce a relation between the constants in (1) and (2).
For applying the Ampere-Maxwell law we choose as the closed loop
this rectangle in the $yz$ plane.
Then we can calculate the change rate of the electric flux $\Phi_E$
appearing on the right side of (3) with the $\vec{E}$ field from (1).
$$\begin{align}
\frac{d\Phi_E(t)}{dt}
&=\frac{d}{dt}\int\vec{E}(z,t)\cdot d\vec{A} \\
&=\frac{d}{dt}\int_0^l dy \int_0^{\lambda/4}dz\ E_0\cos(kz-\omega t) \\
&=\int_0^l dy \int_0^{\lambda/4}dz\ E_0\frac{d}{dt}\cos(kz-\omega t) \\
&=\int_0^l dy \int_0^{\lambda/4}dz\ E_0\omega\sin(kz-\omega t)
\end{align}$$
For simplicity we consider this especially for $t=0$:
$$\begin{align}
\frac{d\Phi_E(t=0)}{dt}
&=\int_0^l dy \int_0^{\lambda/4}dz E_0\omega\sin(kz) \\
&=lE_0\omega\left[-\frac{1}{k}\cos(kz)\right]_{z=0}^{z=\lambda/4} \\
&=lE_0\frac{\omega}{k}\left[-\cos(kz)\right]_{z=0}^{z=\lambda/4}
&\text{remember }k=\frac{2\pi}{\lambda} \\
&=lE_0\frac{\omega}{k}\left(-\cos\left(\frac{\pi}{2}\right)+\cos(0)\right) \\
&=lE_0\frac{\omega}{k}(0+1)
&\text{remember }c=\frac{\omega}{k} \\
&=lE_0c \tag{4}
\end{align}$$
The loop integral on the left side of (3) is easier to calculate.
Again for simplicity we calculate it only for $t=0$.
Then only the left edge (at $z=0$) of the rectangular loop contributes to the integral.
$$\begin{align}
&\oint\vec{B}(z,t=0)\cdot d\vec{l} \\
&=\int_0^l dy\ B_0 \cos(kz-\omega t) \\
&=\int_0^l dy\ B_0 \\
&=lB_0 \tag{5}
\end{align}$$
Inserting the results (4) and (5) into the Ampere-Maxwell law (3) we get
$$lB_0=\mu_0\epsilon_0 lE_0c$$
or
$$B_0=\mu_0\epsilon_0 E_0c \tag{6}$$
The EM wave also needs to satisfy Faraday's law.
$$\oint\vec{E}\cdot d\vec{l} =
-\frac{d}{dt}\underbrace{\int\vec{B}\cdot d\vec{A}}_{\Phi_B}. \tag{7}$$
We can use this law to deduce one more relation between the constants in (1) and (2).
For applying Faraday's law we choose as the closed loop
this rectangle in the $xz$ plane.
Then calculations very similar to the above yield
$$\frac{d\Phi_B(t=0)}{dt}=-lB_0c \tag{8}$$
and $$\oint\vec{E}(z,t=0)\cdot d\vec{l}=lE_0 \tag{9}$$
Inserting the results (8) and (9) into Faraday's law (7) we get
$$lE_0=lB_0c$$
or
$$E_0=B_0c \tag{10}$$
Now we can combine (6) and (10) and find
$$c=\frac{1}{\sqrt{\epsilon_0\mu_0}}$$