If Logan "got his adamantium" in 1979 - which he didn't - then that would mean X1 takes place roughly around 1994, and it doesn't. The original trilogy films take place in the "not too distant future", meaning they take place in the year they're released or not too far afterward. They didn't plan these films to be watched years before they were released by some time traveling movie-goers...
If the prequels and spin-offs don't work into the timeline of the original trilogy, then you can't use them to redirect when the films were originally supposed to happen. It's fine if you want to work XO:W into your continuity, but it disrupts a lot in the other films. I certainly wouldn't base my timeline around it.
I'm fairly certain the connection between Alex and Scott will never be explored; not unless we get another FC-cast film after DoFP introducing Scott. But to be honest, I'm fine if they don't explain it. It'd likely be convoluted anyway. Just like I'm fine if they don't explain the connection between Mystique and Nightcrawler, though I think it'd add a lot to Mystique's story and character, and a nice way to lightly fold Nightcrawler back in the mix.
On an unrelated-ish note, I'm glad that most people aren't including the official games (barring the irrelevant 'X2: Wolverine's Revenge') in the continuity because then Nightcrawler would be the son of John Wraith. No, thank you.
It's simple, really.
There are some minor errors and contradictions in the continuity, no greater in the X-Men film series than in any other expansive series of films. Star Wars has continuity errors and contradictions just as big, if not bigger, than anything found in the X-Men films.
Certain pieces of dialogue from X-Men, like "15 years" (in regards to Logan and Stryker), Xavier and Magneto meeting at 17, and a couple things from X-Men: The Last Stand and X-Men Origins: Wolverine, like Xavier walking when recruiting Jean Grey, or recruiting Cyclops, Emma Frost, and the other students, respectively, and other minor things like various versions of Emma Frost, Beast, or Bolivar Trask, are simple errors. They don't break a timeline, they are simply things that people had better ideas about later on down the line.
The continuity isn't broken. It's not irreparable. It doesn't even need to be repaired in the first place. It is what it is.
Just accept that a couple small scenes, and a couple pieces of dialogue don't line up, and the movies flow together just fine.
For X-Maniac, wanting a timeline, it's simple:
X-Men: First Class (1963) -> X-Men Origins: Wolverine (1973-1979, or 1975-1981) -> X-Men (2012) -> X2 (2012) -> X-Men: The Last Stand (2013)* -> The Wolverine (2014) -> X-Men: Days Of Future Past (2023-new 1973)
*Marked X-Men 3 in 2013 to account for the new President from X2. Timing would apply to the real world, as an election would be held in 2012, with a new President taking oath in 2013. Plus, with Alkali Lake being all snowy in X2, and not so snowy in X-Men 3, you could say that X2 takes place in winter of 2012, with X-Men 3 taking place in spring or summer of 2013.