To show that $E'$ is closed, we will show $X\setminus E'$ is open. If $x \in X\setminus E'$, then there is $B(x,r) \subseteq X\setminus E$. Then for all $y \in B(x,r)$ since $B(x,r)$ is open there is $B(y,r_2)\subseteq B(x,r)\subseteq X \setminus E$ so $y \in X \setminus E'$ as well. It follows that $x$ is an interior point of $X\setminus E'$, and so $X\setminus E'$ is open, and $E'$ is closed.
Now we show $E$ and $\overline{E}$ have the same limit points. Clearly $E' \subseteq \overline{E}'$ since if every $B(x,r)$ contains an element of $E$ different from $x$, then that element is also an element of $\overline{E}$. Conversely, suppose $B(x,r)$ contains an element $y$ of $\overline{E}$. Since $B(x,r)$ is open, we may choose $B(y,r_2)\subseteq B(x,r)$ and by making $r_2<d(x,y)$ smaller if necessary we may ensure $x\notin B(y,r_2)$. Then since $y \in \overline{E}$ we may choose $z \in E \cap (B(y,r_2)\setminus\{y\})$. Then $z \in E \cap (B(x,r) \setminus \{x\})$ which completes the proof.