Your chronological order might have a few other problems like where do time travel stories fit in (e.g. The Voyage Home, First Contact, Trials and Tribble-ations).
When it comes to resolving plot conflicts between series...
For example in TOS Kirk is the one who comes across the Gorn, while in SNW it's Pike the comes across them.
Based on Kirk's dialogue, we assumed he was the first to come across the Gorn. Specifically:
- I face a creature the Metrons called a Gorn.
- I'm engaged with a creature apparently called a Gorn.
So I have two ways I resolve this internally. The first, I reinterprete what I originally understood from the original dialogue. In this case it would be that the Gorn Kirk faces looks unlike any Gorn he had seen in the past (this one has no tail, it moves slow, and it looks weirdly like a human in a rubber suit) so he doesn't believe the Metrons when they call it a Gorn.
Sometimes reinterpreting canon is easy, other times (like this Gorn example) it's more of a stretch, so I usually resolve canon conflicts by telling myself that these shows are creative interpretations of stories that are restricted by their real world technologies and world views. For example, in The Cage, Pike says he's not used to having women on his bridge. I just interpret that as a 60s writer writing a 60s man's viewpoint being said by a 60s male actor. The current Pike is the same Pike but he doesn't have that attitude because the story is not being told in the 60s anymore.
I actually knew that. I was just trying to make a funny. But it failed.