。
She was aching all over.
Literal
She [topic-は] body-throughout [subject-が] was-hurting.
体中 ('throughout the body, all over the body') uses the suffix ~中 (じゅう, not ちゅう) for 'throughout / all of.' Productive: 一日中 ('all day'), 世界中 ('all over the world'), 学校中 ('throughout the school'). 痛む is a slightly more poetic / literary verb for 'to hurt, ache' than the i-adjective 痛い; 痛んでいた is the past resultative — 'was in a state of aching.' The が marks the body part as the subject of pain — Japanese's standard pain-grammar.