What is the correct word order between "have/had", "been", and "already" in statements?

word-order

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.

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