She’d (had) been working for a big company for 9 years before starting working. (A progressive activity from one point in the past to another – the emphasis is on the activity that was ongoing for 9 years. It is plausible that the speaker will proceed to provide further information in the context of her work in the company and the skills she had acquired).

She had worked for a big company before she started working for Samsung. (experience\informative – the emphasis is on the fact that this action had been completed before she started working for Samsung. It is pointed out that she possessed the necessary experience to have made her a good fit).    

He had been working with Jack for 9 years before going into business with him. They spent a lot of time together and got to know each other very well. I think it was a good choice for them to work together. (An ongoing action that had been performed for 9 years before the point in time when he and Jack started working together. Notice how it is very natural to add additional details about their acquaintance as the focus is on the activity).

He had known Jack for 9 years before he went into business with him. (A state that was true for 9 years before a certain point in time in the past. The word “to know” is a verb but a stative one which describes a situation that was true for 9 years before they went into business together).

You hadn’t been doing your homework and that’s why you failed on your test. (A process of not engaging in a certain activity – the emphasis here is on someone who fails to do their homework repeatedly and how that influences a certain point in the past. A description of how this deficiency harmed the student’s ability to succeed on a test or at school is a sensible continuation).

You hadn’t done your homework and that’s why the teacher scolded you. (A task that had not been completed before a certain point in the past – when the lesson took place and the teacher scolded the student as a result).

I had been preparing the food for 2 hours and it was too late for me to start making the cake too, I was also very tired by the time the party was about to start. (the speaker uses the Past Perfect to provide background information for the time when the party was about to start and was had preceded it – the focus is the activity and how it influenced that point in time in the Past). 

I had prepared the food, called the guests, but hadn’t made the cake. I was sure that my brother would bring a cake from the shop but that didn’t happen and the party was a big let down. (How many tasks had been completed by a certain point in time in the past – informative\quantitative).

The cost of living had been increasing steadily for a long time and by 2016 people were very worried. They didn’t know for how long this was going to continue. (Progressive change – the emphasis is on the process of increase and how prices repeatedly increased until 2016. The speaker will probably continue by describing how this increase continued and how that posed a problem and what was done to stop this).

The cost of living had gone up by 2016 and people couldn’t afford a house. (The result of change – the emphasis on the fact that the prices have become higher by 2016 and therefore it was harder to get by economically. It is likely that the speaker will proceed to describe how people had to work longer hours as a result of this new situation).

She’d (had) been sitting in class completing the test when the fire alarm went off and everybody was rushed outside. (A progressive action from one point in the past to another – the emphasis is on how long the action had been and the process and not the number of times it occurred, that is also the reason why we provided with additional information about what happened around that action.)

She had taken the test twice and failed before she finally passed it on the third try. (How many times something has happened until a certain point in time in the past – the emphasis is on the number of times she had done the test before she finally passed.)

It smelled of food and there were pots on the stove, somebody had been cooking. (Guessing what preceded a certain activity in the past by noticeable – the emphasis is on the activity that had been happening before that point in the past where we saw the pots on the stove.)

I had cooked dinner and asked everyone to come to the table. It was late and I wanted to make sure the children went to sleep on time. (An action that preceded a certain point in time in the past – the emphasis is on the fact that this action had been completed and it had implication on the described point in time the past. The focus is more on the implications than the action itself.)