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".