May be it helps you to see more easily the way to attack the problem.
The first that you could try it's find or understand the recursive relation behind Floyd-Warshall Algorithm. As the next function $f$.
$$
f(u,v,k) = \begin{cases}
w_{u,v} & k = 0\\
\min\, (\ f(u,v, k-1),\ f(u,k,k-1) + f(k,v,k-1)) & \text{otherwise}
\end{cases}
$$
- $w_{u,v}$ it's the weight of edge from $u$ to $v$ in the direct graph $G$. $\infty$ if that edge doesn't exist.
- $f(u,v,k)$ is the weight of a shortest path from $u$ to $v$ if you consider the first $k$ vertices as intermediates.
To adapt the above function form for your problem, I'd sketched the essence of the problem in the next graph:
- $m_i\in E_0$
- $l_i\in E_1$
- The curly curve is the shortest path considering the first $k-1$ vertices.
- You have a alternate path that consider the $k$ node when you see the pattern (normal-$k$-dashed) lines in the path, or with convention above: (dashed-$k$-normal) line or $(m_i, l_j)^*$ , $(l_i, m_j)^*$ pattern in general.
So the next step it's construct the recursive relation looking the connection between subproblems, and for that you could think for a moment that your function solve the problem for a small size of problem, or instances pattern (follow principle of optimality).
$$
f(u,v,k,i) = \begin{cases}
w_{u,v,i} & k = 0\\
\min\, (\ f(u,v, k-1,i),\ f(u,k,k-1,~i) + f(k,v,k-1,i)) & \text{otherwise}
\end{cases}
$$
- $w_{u,v,i}$ is the weight for the edge in $E_i$ (Note that I change enumeration of $E$ for convenience). $\infty$ if that edge doesn't exist.
- $f(u,v,k,i)$ is the weight of a shortest path that ended up with a edge in $E_i$ that consider the first $k$ vertices as intermediates like the graph above.
- $~i = 0$ if $i = 1$ or $1$ if $i = 0$.
So, the weight of the shortest alternate path from $u$ to $v$ is
$$\min \,(\, f(u, v, |V|, 0),\ f(u, v, |V|, 1) )$$
where $|V|$ is the number of vertices.
Of course, after some work, you could notice that:
- It's possible delete parameter $k$
- you could implement iterative version or use a memorization technique.
- Other details, that I'm forgiving. It's late.
I'd wrote a python code/ and input test file if you can play with that. But, Here, it's not important.