Ответ:

1. She had been running since 6 AM.

Had she been running since 6 AM?

2. It had been raining cats and dogs for several hours.

Had it be running cats and dogs for several hours?

3. She had been waiting for him for an hour.

Had she been waiting for him for an hour?

4. We had been travelling for 2 weeks.

Had we been travelling for 2 weeks?

;)