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  1. He was dead by the time the doctor arrived
  2. 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?

  1. After he had finished his home work, he went out.
  2. 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.

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    To say "He had been dead" implies that he is now no longer dead - this would be used in phrases like "He had been sleeping" or "He had been working". You could fix this by saying "He had been dead for three hours by the time the doctor arrived" for example. – Max Williams Oct 3 '16 at 9:22
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The perfect aspect is a narrative device which enables the person telling a story to mention at a certain point in time an event which happened earlier (in a flashback).

In sentence 3, the time is when he went out and the time clause after he had finished his homework mentions an earlier event.

Sentence 4 is a simplification of sentence 3:

since the link word/conjunction after 'does the job' of indicating that finishing the homework is anterior to going out, it feels redundant to indicate that same anteriority by means of a past perfect, hence the simplification to a past simple.

Then, there is a difference between to be dead, a situation, a state verb, found in the first two sentences and to finish your homework, an action, a dynamic verb, found in the last two sentences.

The situation to be dead still existed at the moment the doctor arrived, so no anteriority, no perfect.

Things would have been different if you had used the dynamic verb to die; the first sentence would have been incorrect then, not the second one:

  1. *He died by the time the doctor arrived.

  2. He had died by the time the doctor arrived.

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There is a good explanation of tenses in this answer: https://english.stackexchange.com/a/21847/198768

As Max Williams says, the person is still dead. Hence, use the first sentence.

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In the first sentence, it implies that "he" recently died. In the second example, it is implied that he has been dead for some length of time, which is not stated; it also implies that he, who had been dead, is now alive. Because this is presumably not the meaning intended, a better choice of words could be "He had been dead x amount of time before the doctor arrived." However, in the third example, "had finished" is a past perfect tense verb phrase, whereas "finished" is merely past tense. I believe the correct one is number four.

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