Every day after school, I waited for her at the bookstore.
Literal
Every-day, after-school [at-に] I [topic-は] that bookstore [at-で] her [object-を] waited.
放課後 ('after school') is a compound — 放 (release) + 課 (lesson) + 後 (after). で marks the bookstore as the location of waiting. を with 待つ marks the person being waited for.