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She was brooding over the unhappy days she had spent there.
Literal
She [topic-は] there [at-で] spent unhappy days [object-を] sulkily was-thinking.
そこで過ごした不幸な日々 is a packed noun phrase: a relative clause (そこで過ごした, 'that she spent there') plus a な-adjective (不幸な, 'unhappy') both modifying 日々 ('days'). 日々 is the doubled-kanji plural for 日, written with the iteration mark 々, and reads as ひび — common in literary or somewhat poetic register. くよくよ is a 擬態語 (state mimetic) for unproductive brooding, dwelling on regrets, fretting over things you can't change — paired with 考える it gives a clear picture of unhealthy rumination. The と after くよくよ is the adverbial と, attaching mimetics to verbs.