[proofplan]
We prove the contravariant statement directly from naturality, without invoking Yoneda as a black box. The two given representations determine a natural isomorphism between the two representable functors, and evaluating it at the identity morphisms produces inverse arrows $A\to B$ and $B\to A$. Naturality then shows that the natural isomorphism is exactly postcomposition with the arrow $A\to B$, which gives both the required compatibility and uniqueness. For the covariant statement, we construct the natural isomorphism between $\operatorname{Hom}_{\mathcal C}(A,-)$ and $\operatorname{Hom}_{\mathcal C}(B,-)$ directly, evaluate it at $\operatorname{id}_A$ to obtain the arrow $B\to A$, and then write out the inverse and uniqueness computations in the covariant composition order.
[/proofplan]
[step:Construct the natural isomorphism between the representable functors]
For each object $X\in\mathcal C$, define a map
\begin{align*}
\Theta_X:\operatorname{Hom}_{\mathcal C}(X,A)&\to \operatorname{Hom}_{\mathcal C}(X,B) \\
g&\mapsto \Psi_X^{-1}(\Phi_X(g)).
\end{align*}
Since $\Phi_X$ and $\Psi_X$ are bijections for every $X$, each $\Theta_X$ is a bijection. The family $\Theta=(\Theta_X)_{X\in\mathcal C}$ is natural because it is the composite natural isomorphism
\begin{align*}
\operatorname{Hom}_{\mathcal C}(-,A)\xrightarrow{\Phi}F\xrightarrow{\Psi^{-1}}\operatorname{Hom}_{\mathcal C}(-,B).
\end{align*}
Thus for every morphism $u:Y\to X$ in $\mathcal C$ and every morphism $g:X\to A$,
\begin{align*}
\Theta_Y(g\circ u)=\Theta_X(g)\circ u.
\end{align*}
[/step]
[step:Recover the comparison morphism by evaluating at the identity]
Define the morphism $f:A\to B$ by
\begin{align*}
f:=\Theta_A(\operatorname{id}_A).
\end{align*}
We claim that $\Theta_X$ is postcomposition with $f$ for every object $X$. Let $X\in\mathcal C$ and let $g:X\to A$ be a morphism. Applying naturality of $\Theta$ to the morphism $g:X\to A$ and the element $\operatorname{id}_A\in\operatorname{Hom}_{\mathcal C}(A,A)$ gives
\begin{align*}
\Theta_X(\operatorname{id}_A\circ g)=\Theta_A(\operatorname{id}_A)\circ g.
\end{align*}
Since $\operatorname{id}_A\circ g=g$ and $\Theta_A(\operatorname{id}_A)=f$, this becomes
\begin{align*}
\Theta_X(g)=f\circ g.
\end{align*}
By the definition of $\Theta_X$, this is equivalent to
\begin{align*}
\Psi_X^{-1}(\Phi_X(g))=f\circ g.
\end{align*}
Applying the bijection $\Psi_X$ to both sides gives
\begin{align*}
\Phi_X(g)=\Psi_X(f\circ g).
\end{align*}
This is the required compatibility.
[/step]
[step:Construct the inverse morphism in the opposite direction]
Define, symmetrically, for each object $X\in\mathcal C$ a map
\begin{align*}
\Lambda_X:\operatorname{Hom}_{\mathcal C}(X,B)&\to \operatorname{Hom}_{\mathcal C}(X,A) \\
k&\mapsto \Phi_X^{-1}(\Psi_X(k)).
\end{align*}
The family $\Lambda=(\Lambda_X)_{X\in\mathcal C}$ is the inverse natural isomorphism to $\Theta$, because for every object $X$,
\begin{align*}
\Lambda_X=\Theta_X^{-1}.
\end{align*}
Define the morphism $e:B\to A$ by
\begin{align*}
e:=\Lambda_B(\operatorname{id}_B).
\end{align*}
Let $X\in\mathcal C$ be an object and let $k:X\to B$ be a morphism. Applying naturality of $\Lambda$ to the morphism $k:X\to B$ and the element $\operatorname{id}_B\in\operatorname{Hom}_{\mathcal C}(B,B)$ gives
\begin{align*}
\Lambda_X(\operatorname{id}_B\circ k)=\Lambda_B(\operatorname{id}_B)\circ k.
\end{align*}
Since $\operatorname{id}_B\circ k=k$ and $\Lambda_B(\operatorname{id}_B)=e$, this becomes
\begin{align*}
\Lambda_X(k)=e\circ k.
\end{align*}
Now evaluate the identities $\Lambda_A\circ\Theta_A=\operatorname{id}_{\operatorname{Hom}_{\mathcal C}(A,A)}$ and $\Theta_B\circ\Lambda_B=\operatorname{id}_{\operatorname{Hom}_{\mathcal C}(B,B)}$ at the identity morphisms. First,
\begin{align*}
\operatorname{id}_A
&=\Lambda_A(\Theta_A(\operatorname{id}_A)) \\
&=\Lambda_A(f) \\
&=e\circ f.
\end{align*}
Second,
\begin{align*}
\operatorname{id}_B
&=\Theta_B(\Lambda_B(\operatorname{id}_B)) \\
&=\Theta_B(e) \\
&=f\circ e.
\end{align*}
Therefore $f:A\to B$ is an isomorphism with inverse $e:B\to A$.
[/step]
[step:Prove uniqueness of the compatible isomorphism]
Let $f':A\to B$ be any morphism satisfying
\begin{align*}
\Phi_X(g)=\Psi_X(f'\circ g)
\end{align*}
for every object $X\in\mathcal C$ and every morphism $g:X\to A$. Taking $X=A$ and $g=\operatorname{id}_A$, we obtain
\begin{align*}
\Phi_A(\operatorname{id}_A)=\Psi_A(f'\circ \operatorname{id}_A)=\Psi_A(f').
\end{align*}
By the definition of $f$, we also have
\begin{align*}
\Phi_A(\operatorname{id}_A)=\Psi_A(f).
\end{align*}
Since $\Psi_A:\operatorname{Hom}_{\mathcal C}(A,B)\to F(A)$ is injective, it follows that
\begin{align*}
f'=f.
\end{align*}
Thus the compatible isomorphism $f:A\to B$ is unique.
[/step]
[step:Construct the covariant comparison morphism directly]
Now suppose $F:\mathcal C\to\mathbf{Set}$ is represented by both $(A,\Phi)$ and $(B,\Psi)$, with natural isomorphisms
\begin{align*}
\Phi:\operatorname{Hom}_{\mathcal C}(A,-)\xrightarrow{\cong}F,
\qquad
\Psi:\operatorname{Hom}_{\mathcal C}(B,-)\xrightarrow{\cong}F.
\end{align*}
For each object $X\in\mathcal C$, define a map
\begin{align*}
\Theta_X:\operatorname{Hom}_{\mathcal C}(A,X)&\to \operatorname{Hom}_{\mathcal C}(B,X) \\
h&\mapsto \Psi_X^{-1}(\Phi_X(h)).
\end{align*}
Since $\Phi_X$ and $\Psi_X$ are bijections for every object $X$, each $\Theta_X$ is a bijection. The family $\Theta=(\Theta_X)_{X\in\mathcal C}$ is the composite natural isomorphism
\begin{align*}
\operatorname{Hom}_{\mathcal C}(A,-)\xrightarrow{\Phi}F\xrightarrow{\Psi^{-1}}\operatorname{Hom}_{\mathcal C}(B,-).
\end{align*}
Thus for every morphism $u:X\to Y$ in $\mathcal C$ and every morphism $h:A\to X$,
\begin{align*}
\Theta_Y(u\circ h)=u\circ \Theta_X(h).
\end{align*}
Define the morphism $f:B\to A$ by
\begin{align*}
f:=\Theta_A(\operatorname{id}_A).
\end{align*}
Let $X\in\mathcal C$ be an object and let $h:A\to X$ be a morphism. Applying naturality of $\Theta$ to the morphism $h:A\to X$ and the element $\operatorname{id}_A\in\operatorname{Hom}_{\mathcal C}(A,A)$ gives
\begin{align*}
\Theta_X(h\circ\operatorname{id}_A)=h\circ\Theta_A(\operatorname{id}_A).
\end{align*}
Since $h\circ\operatorname{id}_A=h$ and $\Theta_A(\operatorname{id}_A)=f$, this becomes
\begin{align*}
\Theta_X(h)=h\circ f.
\end{align*}
By the definition of $\Theta_X$, this is equivalent to
\begin{align*}
\Psi_X^{-1}(\Phi_X(h))=h\circ f.
\end{align*}
Applying the bijection $\Psi_X$ to both sides gives
\begin{align*}
\Phi_X(h)=\Psi_X(h\circ f).
\end{align*}
This is the required covariant compatibility.
[/step]
[step:Verify that the covariant comparison morphism is an isomorphism]
Define, symmetrically, for each object $X\in\mathcal C$ a map
\begin{align*}
\Lambda_X:\operatorname{Hom}_{\mathcal C}(B,X)&\to \operatorname{Hom}_{\mathcal C}(A,X) \\
k&\mapsto \Phi_X^{-1}(\Psi_X(k)).
\end{align*}
The family $\Lambda=(\Lambda_X)_{X\in\mathcal C}$ is the inverse natural isomorphism to $\Theta$, because for every object $X$,
\begin{align*}
\Lambda_X=\Theta_X^{-1}.
\end{align*}
Define the morphism $e:A\to B$ by
\begin{align*}
e:=\Lambda_B(\operatorname{id}_B).
\end{align*}
Let $X\in\mathcal C$ be an object and let $k:B\to X$ be a morphism. Applying naturality of $\Lambda$ to the morphism $k:B\to X$ and the element $\operatorname{id}_B\in\operatorname{Hom}_{\mathcal C}(B,B)$ gives
\begin{align*}
\Lambda_X(k\circ\operatorname{id}_B)=k\circ\Lambda_B(\operatorname{id}_B).
\end{align*}
Since $k\circ\operatorname{id}_B=k$ and $\Lambda_B(\operatorname{id}_B)=e$, this becomes
\begin{align*}
\Lambda_X(k)=k\circ e.
\end{align*}
Now evaluate the identities $\Lambda_A\circ\Theta_A=\operatorname{id}_{\operatorname{Hom}_{\mathcal C}(A,A)}$ and $\Theta_B\circ\Lambda_B=\operatorname{id}_{\operatorname{Hom}_{\mathcal C}(B,B)}$ at the identity morphisms. First,
\begin{align*}
\operatorname{id}_A
&=\Lambda_A(\Theta_A(\operatorname{id}_A)) \\
&=\Lambda_A(f) \\
&=f\circ e.
\end{align*}
Second,
\begin{align*}
\operatorname{id}_B
&=\Theta_B(\Lambda_B(\operatorname{id}_B)) \\
&=\Theta_B(e) \\
&=e\circ f.
\end{align*}
Therefore $f:B\to A$ is an isomorphism with inverse $e:A\to B$.
[/step]
[step:Prove uniqueness in the covariant case]
Let $f':B\to A$ be any morphism satisfying
\begin{align*}
\Phi_X(h)=\Psi_X(h\circ f')
\end{align*}
for every object $X\in\mathcal C$ and every morphism $h:A\to X$. Taking $X=A$ and $h=\operatorname{id}_A$, we obtain
\begin{align*}
\Phi_A(\operatorname{id}_A)=\Psi_A(\operatorname{id}_A\circ f')=\Psi_A(f').
\end{align*}
By the definition of $f$, we also have
\begin{align*}
\Phi_A(\operatorname{id}_A)=\Psi_A(f).
\end{align*}
Since $\Psi_A:\operatorname{Hom}_{\mathcal C}(B,A)\to F(A)$ is injective, it follows that
\begin{align*}
f'=f.
\end{align*}
Thus the compatible isomorphism $f:B\to A$ is unique, and the covariant case completes the proof of the theorem.
[/step]