Вот заполненные предложения с раскрытыми скобками и изменёнными глаголами в нужную видовременную форму:
The terrible hurricane had destroyed all the houses by that time.
When the professor came, the students had already collected their thoughts.
Had you already found the documents when they came?
Where did you spend your summer holidays?
He had finished his work by 5 pm the day before yesterday.