Hi TargetMBA007.
One thing to keep in mind is that, the point in answering SC questions is to find clear flaws in sentences to eliminate choices.
So, the GMAT is not going to present sentence versions that mention three events and force us to have in mind some ideal way of presenting three events.
Rather, the sentence versions will be either clearly logical or clearly illogical.
So, you don't need to worry about knowing the ideal answers to the questions you asked above. Rather, you can plan to analyze the sentence versions you see on a case by case basis to determine whether the use of the past perfect in them is logical, which should be pretty clear if you understand the basics of how the past perfect works.