Real analysis, including set theory, can be formalised within ZFC. As a first-order theory, ZFC has a countable model by the Löwenheim-Skolem theorem, so the answer to your question is yes.
You ask whether there is a "logic for calculus", which is a little bit misleading: we usually think of a logic as a language together with a proof system and a semantics. First and second order logic are logics or formal systems under this description.
What is needed for calculus in addition to the basic formal system is a signature consisting of those non-logical constants required to pick out those relations, functions and constant elements which we would need to refer to in order to axiomatise the structures involved (in this case, the complete ordered field), and a set of axioms sufficient to prove the theorems of calculus.
As I said above, the background theory employed is usually that of set theory, but in fact that's not necessary: one could drop the powerset axiom and in its place just assert the existence of $\mathbb{R}$, and perhaps the set of functions $2^\mathbb{R}$, depending on how much one wanted to prove.