Ok here's the final timeline I've made after rereading the entire canon and making notes on dates. This does not apply to any fanfic I've written, which play by their own rules. This is just what I've worked out from the Holmes stories themselves, but attempting to make chronological sense. I will use the four-letter abbreviations by Jay Finley Christ, to save typing.
In the "Adventures" stories, Holmes and Watson keep referring between cases as if they happened in order, but I ignore those references as Watson self-promoting, just like in SIGN he keeps referring to STUD as if it was recent, rather than years ago, and pretends that the Baker Street Irregulars haven't aged. As I said before, Watson lies out of discretion.
In SPEC for example, Watson specifically states that he could not publish it until after the lady (Helen Stoner) died. In other cases, the principle people have not yet died, so Watson could be changing names and dates out of discretion for the clients. That's the only way to make GLOR make sense, that Watson substituted the Crimean War from 1855 instead of a war from 1845, so that the real Victor Trevor cannot be identified. Holmes could have asked Watson to do so, for the sake of his college friend. He has been aware since the end of STUD that Watson will publish his cases, and in MUSG Holmes even affectionately calls Watson his biographer, so it's an known factor.