Let $\mathcal{C}$ be a small category, and $A, B \in \mathcal{C}_0$ objects of $\mathcal{C}$. Suppose that for every $X ∈ \mathcal{C}_0$ we have bijections $f_X : \text{Hom}_{\mathcal{C}}(A, X) \tilde\to \text{Hom}_{\mathcal{C}}(B, X)$ such that postcomposition with every $g : X \to X'$, 'commutes with the $f_X$': $$ (g \circ -) \circ f_X = f_{X'} \circ (g \circ -). $$ That is, for each $h \in \text{Hom}_{\mathcal{C}}(A, X)$, we have $$g \circ f_X(h) = (g \circ -) \circ f_X(h) = f_{X'} \circ (g\circ -)(h) = f_{X'}(g \circ h). $$ Everything typechecks, so it must be right ;).
All this is to say that there exists a natural transformation $\mu \in [\mathcal{C}, \textbf{Set}]_1$ between $\text{Hom}_{\mathcal{C}}(A, -)$ and $\text{Hom}_{\mathcal{C}}(B, -)$, namely
$$\mu = \left(f_X : \text{Hom}_{\mathcal{C}}(A, X) \tilde\to \text{Hom}_{\mathcal{C}}(B, X) \right)_{X \in \mathcal{C}_0} : \text{Hom}_{\mathcal{C}}(A, -) \, \tilde\Longrightarrow\, \text{Hom}_{\mathcal{C}}(B, -). $$ As it is 'point-wise' an isomorphism (of sets), it is a natural isomorphism.
I always get a bit confused around opposite categories, but does this allow me to immediately write down the natural isomorphism
$$\mu^{\text{op}} : \text{Hom}_{\mathcal{C}^{\text{op}}}(B, -) = \text{Hom}_{\mathcal{C}}(-, B) \, \tilde\Longrightarrow \, \text{Hom}_{\mathcal{C}}(-, A) = \text{Hom}_{\mathcal{C}^{\text{op}}}(A, -)\,? $$
If so, is this an isomorphism in the functor category $[\mathcal{C}, \textbf{Set}]^\text{op} $? And is that $[\mathcal{C}^\text{op}, \textbf{Set}]$?
What I ultimately want is to use the fully faithfulness of the Yoneda embedding $y : \mathcal{C} \to [\mathcal{C}^\text{op}, \textbf{Set}]$ to prove that $A \cong B$ in $\mathcal{C}$. However, what I have seems to be an isomorphism between something to the tune of $y^\text{op}(A)$ and $y^\text{op}(B)$ or $y(A)^\text{op}$ and $y(B)^\text{op}$, but I'm not sure how to interpret that or if that's in fact correct.
I feel like I'm almost there, but the dualising keeps confusing me and I can't find the mistake.
EDIT: perhaps the question just boils down to whether $\text{Hom}_{\mathcal{C}}(B, -)^{\text{op}} = \text{Hom}_{\mathcal{C}^{\text{op}}}(B, -)$ as functors.
Note that the $\mu^{op} : Hom_{\mathcal{C}}(B,-) \rightarrow Hom_{\mathcal{C}}(A,-)$ need not be a natural transformation. This is just an arrow in the dual category of $[\mathcal{C}, Set]$ corresponding to the arrow $\mu$. You can only say that this is an isomorphism in the dual category.
The categories $[\mathcal{C}, Set]^{op}$ and $[\mathcal{C}^{op}, Set]$ are completely different.
The functor $Hom_{\mathcal{C}}(B,-)^{op} : \mathcal{C}^{op} \rightarrow Set^{op}$ (this is what the opposite of a functor means. Not to be confused with an object of the dual of $[\mathcal{C}, Set]$).
On the other hand, $Hom_{\mathcal{C}^{op}}(B,-) : \mathcal{C}^{op} \rightarrow Set$ is just the functor $Hom_{\mathcal{C}}(-,B)$.
They are different functors.
If you are trying to obtain a "contravariant version" of the Yoneda lemma, you may proceed as follows :
You already have the covariant version.
Now, take an object $B \in \mathcal{C}$ and consider a presheaf $X : \mathcal{C}^{op} \rightarrow Set$. Consider the representable presheaf $Hom_{\mathcal{C}}(-,B)$ and treat it as a covariant functor $Hom_{\mathcal{C}^{op}}(B,-)$. Then, using the covariant version of the Yoneda lemma tells you that $$Nat(Hom_{\mathcal{C}}(-,B), X) = Nat(Hom_{\mathcal{C}^{op}}(B,-), X) \cong XB$$. This is the contravariant version of the Yoneda lemma.
In particular, it says that the Yoneda functor $y : \mathcal{C} \rightarrow [\mathcal{C}^{op}, Set]$ is fully faithful, so that $y$ reflects isomorphisms (as you wanted).
A word of caution : There is something called a co-Yoneda lemma (and deals with tensor products of set-valued functors), which is what actually dualizes the Yoneda lemma.