- He was dead by the time the doctor arrived
- He had been dead by the time the doctor arrived.
As a non-native speaker, I think these two sentences are grammatically right. As for me, #2 seems to be right because of the time sequence. However, a grammar book written a native speaker says #1 would be better than #2 because "was" is a stative verb.
What about the two sentences below?
- After he had finished his home work, he went out.
- After he finished his home work, he went out.
(I think these two are exactly similar in meaning because the conjunction "after" enables me to know which one happened first)
One of my friends, an American studying in university, explained the difference to me as follows:
I think you are over thinking these questions in terms of practical usage. Moreover, the real question I think you are asking is between ASPECT and TENSE. They both intersect in meaning and usage but they differ in terms of the SPEAKER'S opinion/connection on the statement.
Put it simply: Continuous and Perfect tenses deal with Aspect of the Speaker's mind into the sentence.
Your examples with #1 and #2 mean the same thing. However, in more subtle and technical manner, #1 just states the phenomenon. Moreover, some legal writing requires #1 over #2 because it is more neutral. Also stative adjectives and passive construction lifts the responsibility away from the speaker. #2 is the speaker's assessment from his/her point of view of the phenomenon and thus can imply a closer connection to the problem at hand.
So your number #3 and #4 carry the same implication. For everyday usage, there is no difference. Perhaps, British person would use the perfect tense more often and an American speaker rarely uses perfect tense. So keeping the same logic as above, "After he had finished ..." implies his/her perspective and ties the speaker to that phenomenon in some way. The other example with "After he finished ..." is just merely stating the phenomenon at hand.
What do you think about the above explanation ? If you have a different opinion on this, let me know that.