Firstly, I want to say that the "couple a days" was a typo error.
You said that "past perfect" is not a tense, however, in grammar books there is such a thing as past perfect tense. It is not the simple past tense because it tells you what was already done at a particular time in the past and that is the point of the past perfect tense. I was thinking if the simple past could replace the past perfect tense, we would not need it at all.
When I googled on "I thought I had replied" and "I thought I replied", the results seems to more common for the former. I think konungursvia could be right, it should be "I thought I had replied" or "I thought I'd replied" which sounds like "I thought I replied". As you have said, the ESL grammar books also teach "I thought I had replied".
I think he's wrong. I think sometimes some of us teach what's in a book. I teach the language I know, and it's correct language and it's practical teaching - 100% certainty. I understand why I say what I say when I say something is right or wrong. I've explained why both are correct here - simple past and past perfect. And I've explained why it's not absolutely necessary to use the past perfect. I have yet to hear why it should be absolutely necessary to use the past perfect in your example sentence.
It can be "I thought I had replied", but it doesn't have to be. And as to whether or not it has to be, we would need a context.
I said the pluperfect is an antiquated term. It seems such terms do better with Latin based languages or Latin itself.
Just because something is written in one book or a number of books, it does not make opposing views invalid. The past perfect is an aspect of the past tense, and if you ask around, you'll find some others that share this point of view. How many tenses are there? It's impractical to try to teach 10, 12, or 14 different tenses and teach exactly when and how each one is used. Viewing English as a two-tense system is more practical and easier on learners.
If you're writing or studying and you don't know which form of the verb to use, then think about this:
1. Is it past or present?
2. Is it ongoing? Is it progressive in any way?
3. If it's ongoing, is the progressive form of the verb required? Or can the verb itself convey something that is continual or progressive?
3. Is the action something that is a "universal truth" of some sort? In other words, if it's present, should it be simple present?
4. If the action occurred in the past, is it at all relevant now in any way? Will it continue now or into the future.
And so on.
Knowing first whether something is present or past helps in learning which verb form to use instead of attempting to deduce which tense to use out of a number of tenses from which to choose.