I'm trying to show that separation follows from replacement. There are at least two questions here on SE that deal with the question. See The comprehension axioms follows from the replacement schema. and How do the separation axioms follow from the replacement axioms?. I'm not completely satisfied with the answers there.
The basic idea for the proof that most people use seems to be this: Say we have some set $D$ and some formula $\varphi(x)$. To prove separation, we're trying to show that $\{x \in D| \varphi(x)\}$ is a set. Using separation, we need to write a formula $\psi(x,y)$ such that for each $x \in D$ there is exactly one $y$ such that $\psi(x,y)$.
Here's one attempt: $\psi(x,y) = \text{"}x = y \wedge \varphi(x) \text{''}$. IF this formula satisfies the separation axiom, THEN this should work fine. The problem: at least in the version of the separation axiom I know, we need for there to be a unique $y$ for all $x \in D$, such that $\psi(x,y)$. So say $x \in D$ is such that $\neg \varphi(x)$, then $\psi(x,y)$ is always false (and so not true for a unique $y$ as required for the use of replacement).
Here's another attempt: $\psi(x,y) = \text{''}(\{x\}=y \wedge \varphi(x))\vee y=\emptyset \text{''}.$ Now we have a function whose domain is the entire set $D$. And we can use replacement and union to get the set we want. But this requires that both $\emptyset$ and $\{x\}$ are sets. This is the usual argument that they are sets. $D$ is a set, so $\{x \in D| x \not = x\}=\emptyset$ is a set. But that's a straightforward use of separation. We have the same problem for $\{x\}$. Using pairing we get that there is a set $A$ such that $x \in A$, but we don't necessarily have as a result that there is a set that contains only $x$. Of course we could construct this set with $\{y \in A | y = x\}$, but again we've used separation.
It's for the reasons above that I'm not perfectly satisfied with the answers to other questions here on SE. Perhaps I've made some mistake, or there actually is a better answer.