I see no reason why you cannot use $s$ for standard deviation. I have seen this plenty, and the first site that came up when I Googled “standard deviation notation” suggests the notation $s$ as well. This is what I would recommend.
Alternatively (as is also mentioned on the site), you could use $\sigma_S$ for standard deviation and $\sigma(S)$ for sigma algebra. I don’t suppose you would want to resort to $\sqrt{\operatorname{Var}(S)}$ for standard deviation though.
At the end of the day, you are a PhD student, so you understand thoroughly how notation is totally arbitrary, but I understand your desire to make your thesis as unambiguous as possible. Keep in mind that your readership will be comprised of intelligent academics, just like yourself. I think they’ll be able to handle whatever notation you define, especially when it appears in context and when you aren’t afraid to use your words (i.e., don’t rely entirely on notation).