No (in general).
Let $A$ be a non-zero ring and let $S = \mathrm{Spec}(A[T]/(T^2))$. Let $M$ be a free $A$-module of infinite rank, viewed as an $A[T]/(T^2)$-module via the section $A[T]/(T^2) \rightarrow A$ which sends $T$ to $0$.
Take $X_j = \mathrm{Spec}(A[T]/(T^2) \oplus M)$, where $m^2 = 0$ for any $m \in M$, with affine transition maps given by the composition
$$
A[T]/(T^2) \oplus M \rightarrow A[T]/(T^2) \rightarrow A[T]/(T^2) \oplus M.
$$
The limit $X \rightarrow S$ is an isomorphism, hence satisfies $(1),(2),(3)$, while each $X_j$ satisfies none of the properties $(1),(2),(3)$.