It is a very nice question, but unfortunately, this is impossible.
Each member $s\in S$ must be countable, since uncountable sets have accumulation points. And since the hierarchy is accumulating as you go up, the cofinality of the order must be $\omega_1$ (and this is presumably how you deduced CH). It must be at least $\omega_1$, since otherwise we'd have $\mathbb{R}$ as a countable union of countable sets; and the cofinality cannot be larger than $\omega_1$, since otherwise we'd have eventually an uncountable set in the family.
So we may pass to a cofinal suborder, an $\omega_1$ increasing sequence of countable sets $s_\alpha$ with $\bigcup_{\alpha<\omega_1} s_\alpha=\mathbb{R}$, but no $s_\alpha$ has accumulation.
Since every real number shows up eventually, however, at some countable stage all the rationals will be present, but then every $s_\beta$ after that will have many accumulation points, contrary to assumption.