With a stationary loop of wire and field $\vec B$ varying in time it doesn't seem that you'd be able to exploit the Lorentz force, because it's difficult to introduce the velocity $v$. But another configuration may be more helpful, see picture.

A metallic rod (orange) crosses the magnetic lines (light-blue) with a constant velocity $v$ (blue) in the shown direction. It indeed moves the electrons in the rod as your formula $(1)$ says. The rod glides on two metallic tracks (light-gray) which are connected through another rod (light-gray) to form a closed circuit.
Although the field $B$ is constant, the magnetic flux $\Phi$ varies in time, because
$$\Phi_B = \int_{\scriptstyle_S} \mathbf{B} \cdot \text d\mathbf S \tag{i}$$
In our case is the surface $S$ is rectangular, so we can write the flux as $\Phi_B = B S = B L D$, where $D$ is the length of the rod, and $L$ the length of the metallic tracks on which the rod glides.
For the electromotive force we are interested in the flux derivative with time
$$\mathcal E = -\frac {\text d\Phi_B}{\text d t} = v B D. \tag{ii}$$
because $\text dL/dt = -v$.
Now, I believe that my formula $\text {(ii)}$ and your $(2)$ begin to resemble one another. What misses in my $\text {(ii)}$ is the charges $q$, and what has to appear in your $(2)$ is the rod length $D$, which probably is connected with the element of distance $\text d \vec {\ell}$. Also, since in our case the force $\vec F$ in your $(1)$ is along the rod, and the rod velocity $\vec v$ is perpendicular to $B$, the three vectors $\vec F$, $\vec v$ and $\text d \vec {\ell}$ are mutual perpendicular, s.t. the fact that in my $\text {(ii)}$, the vector product does not appear, is not a concern.
At this point I leave the issue to you. I suggest you to think what is the relationship between work $W$ and potential difference $\mathcal E$, and what is the connection between the integration over the loop in your $(2)$ and the quantity $D$ in my $\text {(ii)}$. Hint: in the grey bars no electromotive force is produced.