Friday morning and after the rain that bothered us the night before had stopped we wandered in the record stores of Madrid where literally tons of records were waiting for us.
why had stopped? Wednesday night the rain began and bothered us then it stopped on friday morning and we wandered in the streets of Madrid. So "stopped" is after "bothered" so why past perfect, is it to tell the reader that the rain began first and it bothered us quite a long time after .