First, I think Matteo Tesla proposed a great decomposition that simplifies the problem.
Since OP requested to keep the original MV argument, I decided to complete it.
Let $A=D^3,B$ be as what OP stated in the question.
Determine $H_*(B)$.
$B$ deformation retracts onto the surface of the cube, which consists of six squares with opposite edges identified, i.e., it consists of six $T^2$, whose homology groups are known. Thus, $H_2(B)=\bigoplus_{i=1}^3{H_2(T^2)}=\mathbb{Z}\oplus\mathbb{Z}\oplus\mathbb{Z}$ because opposite faces are identified on the edges, which are also generators of the $2$nd homology group of each $T^2$. Similarly, $H_1(B)=\mathbb{Z}\oplus\mathbb{Z}\oplus\mathbb{Z}$. You can work out these expressions by drawing a flat diagram of the surface of the cube and labelling all equivalence classes. (I can also edit the post to include my drawing if you want...)
Although all of the six faces are tori, their generators of $H_1,H_2$ are identified. A brief way to determine the homology group is just observing this graph, but you can also regard them as different tori and apply MV sequence multiple times, then mod out those identified images, which is more convincing but also more complicated.
Compute $H_*(T^3)$:
We compute $H_3(T^3)$ by a part of MV sequence:
$$0\to H_3(T^3)\overset{\phi_3}{\to}\mathbb{Z}\overset{\psi_3}{\to}\bigoplus_{i=1}^3\mathbb{Z}\to...$$
Your question specifically asks for how to determine $\psi$, so let's focus on that.
Consider the following commutative diagram similar to that of Seifer-Van Kampen Thm
$$
\require{AMScd}
\begin{CD}
H_2(S^2)@>i>>H_2(A)\\
@Vj=\psi VV @VlVV\\
H_2(B)@>k>>H_2(T^3)
\end{CD}
$$
We can ignore $H(A)$ because $A\simeq\{*\}$. And, Let $\alpha,\beta,\gamma$ be the three generators of $H_2(B)$ that are oriented counterclockwise and $\delta$ the generator of $H_2(S^2)$.
Then, $\psi(\delta)=\alpha+\beta+\gamma-\alpha-\beta-\gamma=0$ (use the diagram of the flat surface to help you). Geometrically, the diagram is induced by the chain complex, so $\psi$ actually sends cycles to cycles. $\delta$, as a generator of $H_2(S^2)$ is mapped into $B$ (observing $\delta$ in $B$) it deformation retracts onto the surface. The surface consists of three pairs of faces with opposite orientation when it is identified (you can try to make one, even though they're all oriented counterclockwise in the diagram), so we get the expression as desired because all groups are abelian. Thus $\text{im}(\psi)=0,\text{ker}(\psi)=\Bbb{Z}$, which implies $H_3(T^3)\cong\mathbb{Z}$.
For $H_2(T^3)$, we already know that the map $\mathbb{Z}\oplus\mathbb{Z}\oplus\mathbb{Z}\overset{}{\to} H_2(T^3)$ is surjective because we have $H_2(T^3)\to H_1(S^2)=0$. Now because $\text{im}(\psi)=0$, the map $\mathbb{Z}\oplus\mathbb{Z}\oplus\mathbb{Z}\overset{}{\to} H_2(T^3)$ is also injective. Hence, $H_2(T^3)\cong\bigoplus_{i=1}^3\mathbb{Z}$.
I guess I can stop here to make this post focus on the main problem on that map.