Linguists call the perfect forms "aspect" not tenses, but that's probably not terribly important here.
1) Yes, the sequence of past/present-perfect forms doesn't imply sequence. If the author needs to specify sequence, he/she needs to change the time.
2) In the quoted passage, the last verb IS past-perfect. What makes you think otherwise? He is remembering the aircraft from earlier. Without "had," it would say that another aircraft flew overhead and triggered his memory.
3) I think you have a very good understanding of the English past/present-perfect. I just think someone confused you with bad information on this one sentence.
Aspect does not refer to a difference in the things described. It refers entirely to how the speaker is choosing to refer to the events on that occasion: specifically, on the temporal relationship between the events and other events or points in time.
I was sleeping is focussing on the continuing state (in the past) of my being asleep. It can refer to precisely the same event as I slept or I have slept: the choice is in what we are saying about the event.
In English, for most verbs we use the so-called present continuous to talk about events which are happening at this moment, irrespective of how long they are continuing: She is wearing a jacket usually talks about the fact that at this moment she has a jacket, and says nothing about how long or how often she does so. For most verbs, we use the simple present only for habitual or universal claims: She wears a jacket talks about her habitual apparel. (It may or may not be true that she is wearing a jacket at this moment, but this does not affect whether She wears a jacket is true).
Verbs of perception and mental state usually do not behave in this way, and are used in the simple present (I see, I feel, I remember). They can be used in the continuous, but this is "marked" as linguists say, and expresses a specific meaning: focussing on the immediate currency of the state or perception. But again they do not express a different situation, just a different way of referring to it, with a different focus.
In the past, there are two more options - the perfect (I have seen) and the perfect continuous (I have been seeing). Again, the difference is in what we are focussing on, not in the events described. In I have cleaned my room, we are focussing on the present relevance of the activity, and on the action being completed. But we certainly can say I have been cleaning my room, about the same activity, but with a different focus.
One way to look at this is by considering what questions they might answer.
What have you done today? I have cleaned my room.
Where were you at 2:30 this afternoon? I was cleaning my room.
How did you spend the afternoon? I have been cleaning my room.
Best Answer
The default in reporting speech is to turn verbs that occur in the present tense in the actual words spoken into the past tense and to turn can into could. Doing this produces:
In this case, however, the most satisfactory solution might be to leave the verbs in the reported section as they are, and to introduce them not with asked but with asks.