I think the first and third would be more common, and probably the first sounds a bit more natural than the third. The middle sentence ("I had been already using it...") would be fairly rare, I think, at least among UK speakers.
Note that "By the time that..." would be a bit more natural than "When" here.
Your updated question seems to show a confusion between name and description. There are seven 'Harry Potter' books, but only one book 'Harry Potter and the Philosopher's Stone'. So "The 'Harry Potter' books" could refer to the series of seven, or to a pile of books on the table, but "The 'Harry Potter' book" could only refer to a single copy (unless there is other context), since there is no book called 'Harry Potter'. (That last phrase could equally have been there is no book 'Harry Potter', a better illustration but a more confusing explanation.)
If you are using a term as a name, you put the name last, just as you would normally refer to the user AlexAtNet rather than ?the AlexAtNet user. That explains the book 'Les Miserables', and it can make a real difference; "The '"Quasimodo" book' is actually the book 'Notre Dame de Paris'."
Your other examples are less clear, but I think the same logic applies. A character has only one existence (though billions of instantiations) and so a name, whereas every keyboard has one of each key, so they are given descriptions. Consider "To obtain the character 'a' you will have to press the B key".
And in some cases name or description depends only on whether you use inverted commas (or, as often on this site, italics). 'The 80 port' is normal and 'the port 80' confusing if not wrong, but To reduce confusion I have named the ports on that side; port '1' is on top, and port '80' (the I/O port) beneath.
Best Answer
Usually you would put the is first and the adverb second, unless you wanted to give special emphasis to the word is (as if stressing the word when speaking: "There already is a price tag!")