(Assuming I understand what you're saying.)
When you meet someone for the first time you don't exactly know what they have done elsewhere, right?
But let's say they robbed a train in a nearby city. If you watch the news that's something you'd likely hear about. If you converse with people it might come up in conversation. If the train was carrying something to your city like street lights to replace the ones that fried in a storm, that's something you'd notice and or hear about. You'll know of their work, but not necessarily know it was them. (So in short, it was the result of what the character did that are relevant, not so much the character.)
So basically each individual doesn't act as an omniscient being, but as another person trying to make their way through the world. If they want to influence or be a part of something, they would find out about those things through in world means assuming their character has the motivation for it. On the player side this alleviates the need to be a part of everything to the point that it forces you to break character, but allows you a path to generate leads for yourself to become involved; and on the GM side it allows those that are needed to be a part of everything, to have obvious connections to obvious scenarios and characters, all individually aligned and organized to certain reference points (the characters or the locations) instead of a big muddle mess of trying to shove everything in together at the same time.
Referencing you back to the thread I posted, I generated individual paths to choose from within the city, all with different ongoings at the time, all that held a degree of importance, though would not necessarily conflict with one another at all times. For instance in one area a man waited to see the person in charge of the city, obviously important. In another area a person was in conflict with the robot guards, important as well in establishing what that detail of the story is like, and also shows that there is a person at odds against the environment, a lead generated by conflict, that could likely affect other areas of the story and the main progression of the story as well. There were also other areas that were obviously important resources, such as the hidden rebellion.
In short, there is no need to reinvent the wheel on structuring a story. Life has already provided you with the perfect structure!
And time fluxing is a problem, the first thing I found out when starting here. On a higher level that is easier to address, by simply creating milestones, objectives, goals that would move the story along. These can be reached by someone doing something to make it happen, or by a timer. On a smaller scale, the events of individual characters are hard to regulate in time, especially when one character needs something different to progress than another, requiring them to be on different time frames. The only idea I can offer to fix that is to ensure that characters interact often, which would constantly force them to sync up their time frames. For instance, the interaction between Vault, Bass, and Saho kept them within the same time frame, before Saho suddenly shot off like a rocket and traveled far off into the future before Vault even had a chance to take a sip of his morning coffee. All I can say about that is offer enough various outlets for roleplaying to slow each one down to near the same speed (other stories, threads, timelines, universes, etc outside of the main plot), and just ignore some of the inconsistencies by condensing them into a single time line in a manner that doesn't cause conflicts.
They have a meeting in the morning and they need to push time forward to conduct it? Oh well, the character that they ran into right afterwards was already operating on that day, the previous day that set up the meeting was in the past. /shrug
Now when both characters interacted with another character that is definitely stuck in one timeline and then those two characters meet each other then.... /shrug /shrug
I can only offer that you conform their timelines to the more important one, but make it less jarring by loosening up the main one and rearranging it in a way where the specifics of time in that case didn't matter.
Alternatively you could conduct a thread with set limits on time, or a strict time table. For instance you can start the thread with the setting and such, and then initiate day 1. Whatever happens until time is moved forward to day 2 happens on day 1. If two people meet and setup a meeting on day 2, they cannot conduct the meeting until day 2. Once sufficient time has passed or enough events have happened or the main event has happened, day two can be initiated. If characters had something they needed to do on day one, they can finish it up, but they will not be interacting with the characters as they are on day 2.
Alternatively, you can set a starting date, and simply require character to track their time as they progress, for instance mentioning the time of day (morning, afternoon, night, etc) and any progressions to another day, for instance moving from day 1 to day 2. That allows more freedom for the individual characters, but as you've noticed freedom causes its own set of problems. For this, someone might be far off in day 15 while someone else is on day 3. If they needed to interact it would be kind of wonky, though no wonkier than not keeping track of it and creating mixed up timelines.
I wish I could put this much thought and effort into my work...