"While Cthulhu stirs in his slumber, investigators have their maximum Sanity and maximum Stamina reduced by 1."
So when he wakes up, surely he's no longer "stirring in his slumber" so the Investigator's maximum Sanity and Stamina should both return to their printed values? You wouldn't actually gain any Sanity or Stamina tokens, just the maximums. Surely?
Otherwise, if "stirs in his slumber" text applis during the Final Battle, then it would also apply for Chaugnar Fagn, Quachil Uttaus, Glaaki and Ghatanothoa, too ...

? And really, the "best" it can do is -1 Sanity, assuming that when First Player token changes hands for any reason, the Dust Decks are reshuffled (2 GOO cancellers, technically you could see 1 investigator get devoured). Chaugnar Faugn to me would penalize you, but if you leave yourself with an unused ES, you deserve to get penalized.