Here are the correct answers for the questions:

9. **C) had done / was having**
The sentence should read: "I had done my homework by 6 o'clock yesterday and when my mother came home I was having supper."

10. **C) had finished / was going**
The sentence should read: "He said that he had finished school and he was going to enter the academy."

11. **B) was / was raining**
The sentence should read: "It was dark and it was raining."