Yuyuko's scenario is before Suika's because the clouds were "starting to form" in Yuyuko's and "concentration three times normal" in Suika's.
Except for Stages 3 and 4, all of Aya's scenarios should happen on different days since she starts with "Today we're going to..."
Reimu's movements on the day of the earthquake are as follows:
Shrine gets destroyed → Alice visits → Goes to see if Marisa is okay → Gets abducted to SDM on the way back → Patchouli's ending (Sakuya been told to warn Reimu) → Youmu visits → Alice and Sakuya's endings (advise Reimu to go to Heaven) → Reimu's scenario starts
Suika is in the background of Alice's ending art, where she is shown rebuilding the shrine though she should only be doing that after the shrine's second destruction. Since the text of Alice's ending doesn't mention Suika, her being there in the art should just be a mistake.