(1) Well, why would you want to require $S$ to be small? It is possible to define inverse limits when both $C$ and $S$ are large, if you like. However, usually if you want to be sure that inverse limits actually exist, you need to assume $C$ is small. For instance, if $S$ is sets, then the formula only makes sense when $C$ is small, since you need the index set $I$ of the product to be a set to be sure the product itself is a set.
(2) Here $a_j$ is an element of $A_j$ for each $j$. Since $m$ is a morphism $j\to k$, $F(m)$ is a morphism $A_j\to A_k$, so $F(m)(a_j)$ is an element of $A_k$. So it makes sense to ask whether $F(m)(a_j)$ and $a_k$ are equal, since they are both elements of $A_k$. A tuple $(a_i)_{i\in I}$ is only an element of the inverse limit set if this condition is true for all $j,k$ and all morphisms $m:j\to k$.