I am now reading Munkres and I had struggled with this problem for a long time. I know that it is an old post but I don't quite understand the answers written by Brian and Daniel (perhaps I am too dumb). So I want to give my own answer for anyone who will have trouble on this problem. My answer is quite similar to drhab's answer.
I will use the following notations:
The "diagonal line" $D = \{(x,x)\,|\, x \in \Bbb{R}\}$.
If $R$ is a relation on $\Bbb{R}$, let $E(R)$ be its equivalence closure, i.e. the smallest equivalence relation on $\Bbb{R}$ that contains $R$. Similarly, let $r(R)$, $s(R)$ and $t(R)$ be it reflexive closure, symmetric closure and transitive closure respectively. For simplicity, we shall write $r(s(S))$ as $rs(S)$ and $r(s(t(S)))$ as $rst(S)$.
Some more general comments about those closures:
Given $S \subseteq \Bbb{R} \times \Bbb{R}$, $r(S)$, $s(S)$, $t(S)$ and $E(S)$ exist since $\Bbb{R} \times \Bbb{R}$ is a reflexive, symmetric and transitive relation that contains $S$ and we can take intersection as in Magidin's answer. So that $T = E(S)$.
In particular, as noted in drhab's answer, $r(S) = S \cup D$ and $s(S) = \{(y,x)\, | \, (x,y) \in S\} \cup S$.
In general, $st(S) \subsetneq ts(S)$. For $\subseteq$, $ts(S)$ is a transitive relation that contains $S$ so that $t(S) \subseteq ts(S)$. And $ts(S)$ is symmetric so that $st(S)\subseteq ts(S)$. But it can be the case that $st(S)$ fails to be transitive.
Similarly, $rst(S), srt(S), str(S), rts(S), trs(S)$ and $tsr(S)$ are all subsets of $E(S)$. By showing $rts, trs, tsr$ satisfy reflexivity, symmetry and transitivity, $E(S) = rts(S)= trs(S)=tsr(S)$ but it can be the case that $rst(S) \subsetneq E(S)$, again it might fail to be transitive.
From question 5(a), $S'$ is an equivalence relation on $\Bbb{R}$ containing $S.$
Let $R = D \cup (0,3)^2$. It is clear that $R$ is an equivalence relation on $\Bbb{R}$. Pick any $(x,y) \in S$. $x \in (0,2) \subseteq (0,3)$ and $y = x +1 \in (1,3) \subseteq (0,3)$. So $(x,y) \in (0,3)^2 \subseteq R$. So that $R$ is another equivalence relation that contains $S$.
We claim that $R \cap S' = E(S)$.
$R'\cap S \supseteq E(S)$: $R, S'$ are equivalence relations containing $S$, so that $R'\cap S$ is also an equivalence relation containing $S$ according to 5(b). Since $E(S)$ is the smallest equivalence relation that contains $S$, $E(S) \subseteq R'\cap S$.
$R\cap S'\subseteq E(S)$: Let $A = \{(x,x+2)\, |\, x \in (0,1) \}$ and $B = A \cup S$.
Claim 1: $S' \cap R \subseteq rs(B)$.
Pick any $(x,y) \in S' \cap R$. $y-x \in \Bbb{Z}$. But $x,y \in (0,3) \implies -3 < y-x < 3$.
Suppose $y - x = 0$. Then $x = y$, so that $(x,y) \in D\subseteq rs(B)$.
Suppose $y - x = 1$. But $y < 3 \implies x = y -1 < 2$. $x \in (0,2)$ and $y = x +1$. So that $(x, y) \in S\subseteq B \subseteq rs(B)$.
Suppose $y - x = 2$. Then $x \in (0,1)$ and $y = x+2$ so that $(x,y) \in A\subseteq B \subseteq rs(B)$.
For the cases $x - y = 1$ and $x-y = 2$, $(y, x) \in rs(B)$ according to the above two cases. But $rs(B)$ is symmetric so that $(x,y) \in rs(B)$.
Claim 2: $B \subseteq t(S) $
Pick any $(x,y) \in A$. Then $x \in (0,1)$. Then $x +1 \in (1,2) \subseteq (0,2)$ and $y = (x+1)+1$. We have $(x,x+1) \in S$ and $(x+1,y) \in S$. So that $(x,y) \in t(S)$ since $t(S)$ is transitive. So $A \subseteq t(S)$ and $S \subseteq t(S)$. Then $ A\cup S=B \subseteq t(S)$.
So that $rs(B) \subseteq rst(S)$. Combining this with claim 1, $S'\cap R\subseteq rs(B) \subseteq rst(S) \subseteq E(S)$.
This complete the proof. In this particular case, we have $rst(S) = E(S)=rs(B) = R\cap S'$. We can draw up $rs(B)$ or $R\cap S'$ to give Brian and Daniel's answer.