It's become apparent to me that many of the mysteries in Fine Structure depend on the precise order in which the stories occur. Time to get systematic. Obviously, this whole post is full of spoilers.
Plot Summaries
Line-breaks indicate flashforwards or flashbacks. I've given characters' full names when we first meet the characters, not when we find out what their full names are.
Forgotten Things in Space (FTiS): Earth is near to uninhabitable. An arkship is launched to Eden.
Calrus (= Mitch Calrus?) discovers FTL travel. Presumably, an FTL ship is dispatched to Eden.
Eden becomes near to uninhabitable. An arkship is launched to Earth.
On Digital Extremities (ODE): Mike Murphy, Seph Baird, Philip Hood, Hugh, Kuang Ching-Yu and others conduct the first A-layer experiment, and discover the carrier wave on A-layer channel one and the messages on channels two and three. They put the messages on the Internet, and the team dissolves.
At least two years later, Ching meets with Mike Murphy and presents him with Jim Akker's walkthrough of the channel 2 message (4kB) and the first 4MB of the channel 3 message (~8TB). Mike Murphy begins work on decoding the rest of the channel 3 message.
[I'd just like to point out, by the way, that 8TB is a preposterous amount of data - the English Wikipedia, for instance, compresses down into a couple of gigabytes, so is probably around 4GB uncompressed. Though UKAPL might well have the gear to store that much data, being physicists - while 8TB is
eight times the amount of raw and processed data collected by JET between 1978 and 1998, it's roughly the amount of data produced by the LHCb in a day.]
Power of Two (Po2): Birth, and subsequent death, of Tzu-Le Chang (Ten). Jason Chilton (Nine) discovers that Ching is able to predict future Births.
Zanjero (Z): Birth of Sixteen, and seeming death of Brent (presumably a Power between Twelve and Fifteen).
Crushed Underground (CU): Rebels led by Nohta Brown seize control of Talmansk Arcology from the Governor (= Mitch Calrus?). Calrus takes them outside, into a sandy, desolate, poisoned, radioactive wasteland. Calrus claims to be terraforming the planet so it will support life again, but it will take thousands of years.
Taphophobia (T): Adrian Ashmore, Anne Poole, Thomas Muoka and others conduct the first experiment in teleportation. The night before, the equipment was struck by lightning. Anne Poole disappears, and Adrian Ashmore is imprisoned for manslaughter.
Eighteen months later, Anne Poole, invulnerable and with a shattered mind, is found in a coal seam. Detective John Haddon begins his involvement with the case.
The Astronomer's Loss (TAL): Despite an astronomer's protests, a mysterious voice blots out the stars, planets and moon.
Amber (A): Haddon informs Ashmore that Anne Poole has been found in the coal seam. Ashmore sketches out a scheme for how this could have happened, claims that he is the only one who could have performed the scheme, but denies that he murdered her. Dr Srin Shapur is assigned to treat Poole's psychosis, and explains Poole's invulnerability to Ashmore. Ashmore is allowed to work on the problem of how Poole became invulnerable. Shapur posits that Poole is now immortal.
Indistinguishable from Magic (IfM): Mitch Calrus meets Seph Baird, demonstrates his phasing powers, and describes his X-ray vision (but gives no demonstration). Seph is still doing her PhD. She agrees to investigate Mitch's powers.
Paper Universe (PU): Shapur has been treating Poole for several months. Ashmore outlines a theory which accounts for Poole's invulnerability and immortality, but not her continued ability to move and think. He suggests that she must have been immortal before the teleportation, and that she was deliberately teleported into the coal seam to get her out of the way. Muoka and Ashmore hints that it's possible that someone or something knew ten times as much teleportation physics as they did at the time.
Exponents (E): Datu Dimasalang (Eleven-to-be) is secretly brought to "Area 51" by Captain Moxon. Ching, who has been informed of his presence by Jason Chilton and Arika McClure (Eight), confronts Moxon and is fobbed off, and then briefs Jerry Kavet, the Tagalog translator, on the Powers and Dimasalang's imminent Birth.
2048: Ching is excluded from the end of Kavet's briefing. Ching goes to the US Medium Preonic Receiver to work on the channel 3 decryption. It is now four years since the events of On Digital Extremities, and between 0.5% and 1% of the message has been decoded (40-80GB). Dimasalang is Born, and immediately murdered by Moxon and his superiors. Ching puts the US MPR out of commission for the next eighteen months, is rescued from the Area 51 guards by Jason and Arika, and says "England" to Jason before their abrupt departure.
Two Killed in "Transporter Accident" (2KiTA): The teleportation experiment from Taphophobia is repeated: again, lightning strikes the building (this time during the experiment), and Philip Hood and Martin Klemperer are teleported 500 feet into the air and fall to their deaths; Alan Jeyrie and Teng Lo are teleported miles into space, in spite of not being in the building at the time (and Teng Lo being in his car, moving at 70mph). Muoka and Ashmore conclude that this is a deliberate attempt by someone with advanced teleportation technology to kill TP research, and Muoka announces that he intends to return to pure theoretical research. Ashmore is still in prison.
The Four Dimensional Man (4DM): Mitch Calrus uses his superpowers to rob a bank, but Seph Baird deduces it's him, persuades him that crime's not worth it, and tells him to return the money.
Crash Zero (C0) In Cahagan, eight hundred years after Crash One, Junior police officer Aks thinks he recognises Yuen (= Anne Poole?) from his history studies, and approaches her, but is rebuffed.
Some weeks later, he visits Professor Gilland, and discusses the Crashes, and the various legends of immortal blonde women. Gillard mentions a recently-discovered monolithic dome in Antarctica which is completely sealed. Gillard warns Aks not to get obsessed with Yuen.
The Nature of the Weapon (NotW): Aks visits Yuen in Bookwreck. Yuen sells him a magazine from immediately before Crash One, roughly eight hundred years before, featuring an interview with Aoni Kulla, who Aks believes to be the same woman as Yuen.
Eight hundred years before, Aoni Kulla retires as Chief Scientific Advisor to the kingdom of Oroth, and is interviewed for the magazine. She claims that the lack of historical evidence shows that the Electromagnetic Project is headed down a blind alley, and that the theory of atoms is not on the list of scientific advances that are known not to cause Crashes.
Aks' partner, Illu, shows Aks a wanted notice for Yuen, who is apparently an extreme anti-Crash Luddite, wanted for murder and sabotage on four continents. Aks and Illu head off to arrest Yuen.
The Big Idea (TBI): A woman (Yuen/Poole?) is dining with her husband, when there is a huge explosion, which apparently devastates the city (and melts her wedding ring). This is presumably a description of Crash Eight.
Aks explains the Crashes and pile of wreckage on which their civilisation is built to Illu.
Scientists fail to either kill a woman or duplicate her invulnerability, so she is buried in a cement-filled mine. She vows to come back and destroy their civilisation single-handedly, and 110 years later does just this. This is possibly in pre-Crash Four Greenland.
Aks predicts that Crash Zero will occur within the next fifty years.
Aoni Kulla visits Quond, the head of the Electromagnetic Project, and tries to convince him to abandon his research into particle physics, first by giving him answers from a previous age, then by telling him about the nuclear weapon that was used to destroy Ytreko. She claims that the Crashes are a mechanism to prevent nuclear war. He intends to continue with his research anyway.
Aks reveals that the magazine was printed on the very day of Crash One.
Chronology
First, some terminology: let's use "Epoch n" to refer to the period between Crash n + 1 and Crash n. So the Aks/Yuen stories occur in Epoch 0, the Quond/Kulla episode occurs in Epoch 1, and so on. Owing to the absence of high-tech wreckage littering the world, I conjecture that the present day is Epoch 8, ie prior to any Crashes. The various references to modern culture (Google, Pink Floyd, etc.) suggest that the Line/A-layer/teleportation stories occur in the present, so we can interpret the dates in the news story in 2KiTA as dates in our system. So, what does that give us?
August 2005: first teleportation experiment (T).
2006: publication of Generating Waveforms in Ambient Neutrality (ODE)
January 2007: discovery of Anne Poole in the coal seam (T).
Mitch Calrus is aware of Anne Poole's condition in IfM, and she's still surrounded by media, so he discovers his powers some time in early 2007, or 2008 at the outside. Seph Baird is doing her PhD at this point (which is apparently "ahead of schedule" - I just about fell off my chair laughing when I read that...). She's meant to be half-way through her PhD in ODE, and it would take some time to construct the preonic receivers after the theoretical results were published in 2006, so the events of ODE probably occur in 2007-2009. Possibly 2006, but I think that's seriously overestimating the pace at which such experiments happen :-) Exponents and 2048 occur four years after ODE, in Year Eleven, so ODE occurs in Year Seven, and the Births started some time between 1999 and 2002. The first TP experiment happens before the publication of Generating Waveforms..., so is unconnected to the A-layer experiments: however, by the time of PU, Muoka and Ashmore appear to be aware of the Eka message and at least some of its contents, so PU probably occurs after Jim Akker's decryption, two years after ODE. Dr Shapur has been treating Poole for "a few months" by the time of PU, so we're probably still in 2007, which would mean that ODE had occurred not later than 2005... which means that either Sam's made a mistake with his timeline, or I have. Much more likely that I have. Ah - I'd forgotten publication delay. As any scientist can tell you, the time between submission of a paper and its eventual publication is totally unpredictable, and can easily be over a year. So, suppose Murphy et al submitted their paper some time in 2004, started work on the preonic receivers, the paper underwent really rigorous peer review and didn't appear until 2006, by which time they'd performed their experiment... that would put Seph Baird in the second or third year of her PhD in 2007, which fits much better with the description of her in IfM and 4DM. So, what does that give us?
1999: Birth of One.
2004: Submission of Generating Waveforms in Ambient Neutrality. Work begins on preonic receivers.
August 2005: First TP experiment (T).
2005: Birth of Six, first known superhuman, in Russia (E).
Early 2006: Murphy et al's paper finally published. A-layer experiment performed (ODE).
2006, some time: Ashmore languishes in prison. Birth of Seven, also in Russia (E).
January 2007: Anne Poole excavated (T, A). Work resumes on TP with accelerated schedule and extra funding (A).
Early 2007: Seph Baird meets Mitch Calrus (IfM).
Mid-late 2007: Mitch Calrus becomes the world's first supervillain (4DM).
2007, some time: Birth and subsequent orphaning of Arika McClure (Eight), in Australia. Ching moves in next door to Jason Chilton.
Late 2007: Jim Akker's decryption of the Eka message (ODE). Ching meets Mike Murphy (ODE). Ashmore proposes explanation for Poole's invulnerability (PU).
2008, some time: Birth of Jason Chilton (Nine) in the Scottish Highlands. Ching goes to Lanzhou.
2009, some time: Birth of Tzu-Le Chang (Ten) in Lanzhou, China. Jason Chilton brings Ching to work at Area 51 (Po2).
2010, some time: Birth and subsequent murder of Datu Dimasalang (Eleven) in Area 51. Ching, Eight and Nine leave Area 51 for England.
2015, some time: Birth of Sixteen, and presumed death of Brent (Z).
Hmmm, not entirely convinced I've got that right. But, that ties On Digital Extremities, Power of Two, Zanjero, Taphophobia, Amber, Indistinguishable from Magic, Paper Universe, Exponents, 2048, Two killed in "transporter accident" and The Four Dimensional Man into present-day Earth. Hmmm. On the other hand, there's very little to connect Zanjero to Earth - he needn't be Sixteen in the same Line.
As for the rest: FTiS and CU both appear to happen after 4DM (assuming the "Calrus" in FTiS is actually Mitch Calrus). I'd guess that FTiS happens after CU, but it could be the other way around. The main events of C0, NotW and TBI appear to happen in that order, and in the flashbacks, Kulla's interview is probably before her meeting with Quond, and Crash One occurs almost immediately after that - the precise time difference depends on Epoch One publication delays, of course. It's not at all clear whether the Calrus stories happen before or after the Crash stories - as
necaris suggested, the Crash stories could occur after Calrus' terraforming has been successful. The only problem I can see with that is how the highly technological society in CU could descend to barbarism once it had left the arcology - a subsequent, non-nuclear, Crash, I suppose.
I should probably put all this stuff into some sort of Hasse diagram, but right now I can't be bothered :-)