What do you guys think?
I think everything happens in the order the stories are unlocked. However, the scope of the incident ebbs and flows in response to the endings of other characters. That just makes the most sense to me, and seriously why in the world would it be written any other way? There is literally no reason to tell the stories out of order. Also, Kokoro's reactions to things changes depending on what's happened to her earlier (ie: she's way more aggressive against Reimu and Marisa, etc).
For reference, I'm the one who made these translations and if you're using my files I should have numbered them so they appear in the order they're unlocked. That's basically the order I think it happens in. I also edited the wiki to list their story routes in this order because I think it's important for them to be presented in the same way the game does. Which is:
Reimu and Marisa: They have no real clue what's going on and nothing gets resolved.
Miko and Byakuren: They actually resolve the incident, albeit temporarily.
Futo and Ichirin: They happen immediately after/during Miko and Byakuren. This is referenced within their routes.
Koishi and Nitori: Kokoro is regressing because Miko and Byakuren's solutions are merely temporary. They offer new, unusual solutions.
Mamizou: She notices that Kokoro is still having problems despite everyone saying they solved it.
Kokoro: Happy ending.