Elantris/Headscratchers

The Seons continued to function after the Reod
The Seons have Aons at their core. When the Aons changed, why didn't all the Seons go as comatose as the Elantrians' Seons?
 * It's strongly implied that there's more going on with the Seons than we think. Note that while an Elantrian's power grows weaker the further he/she is from Elantris, a Seon's does not -- Hrathen is able to use his to communicate with someone on the other side of the world without any problems. Also, Brandon Sanderson has said that if he makes a sequel, it will focus on Seons and what they are -- meaning that there must be a lot about them that has not yet been revealed. In other words, it's very likely that there's a reason for this, but Sanderson just plain didn't have time to go into it -- heck, his annotations mention at least one scene focusing on Seons that ended up on the cutting room floor.
 * There's multiple ways of channeling the Dor, seons are most likely not based on the Elantrian method and thus their power doesn't diminish. Or something like that I would guess.
 * Remember that Raoden found nothing about how Seons are "born" during his exploration of Elantris's surviving records, strongly suggesting that whatever their origin is, it doesn't actually have anything to do with the Elantrians.
 * There is an explanation, but it's rather involved (even by Sanderson's standards) in the entire mythology of the Cosmere. As an attempt to summarize, AonDor existed because of the presence of a Shard of Adonalsium. (Major Sanderson mythos spoiler coming) Seons are Splinters, meaning they are an actual piece of the Shard itself, which can exist independently of the Shard. Also, all of the above is pretty much conjecture, with a few instances of Word of God.

What's with Raoden making the Elantrians work?
While there's something to be said for an activity to keep your mind off pain, having people whose bodies can't heal do manual labor seems really stupid. If their muscles get fatigued from all the exercise, shouldn't they stay fatigued permanently? If their joints get sore from the work, won't their joints ache forever? I mean, c'mon, they've got a guy carving stone by holding a bent nail between his fingers; that's got to cause at least as much pain as writer's cramp, and this is writer's cramp that will never go away. And with people repeating these tasks on a daily basis, the accumulated pain should add up to an insurmountable amount within weeks. Whatever good Raoden's work assignments do in taking the Elantrians' minds of their pain should be far outweighed by all the additional aches they must be accumulating, sending them even farther on the path to becoming Hoed.
 * A Shardholder did it. Muscle fatigue is a function of the digestive/circulatory system. It has to do with the muscles burning sugar faster than the blood can replenish it. It's been established that Elantrians don't have blood, and that, despite their constant hunger, they don't actually need to eat. Apparently their bodies are fueled by the Dor, not by biology. So there's no need to worry about muscle fatigue, cramps, etc.
 * Also it's sort of explicit that working (as in having a role in the community and feeling important) is the only thing that allows the Elantrians to forget their suffering. When Saolin was injured fighting for Raoden he explained that the wound did hurt, but that he knew he'd gained it in service to his people and that it was a good kind of hurt because it reminded him what he fought for. Presumably any other work-related injuries incurred by the New Elantrians would be treated (or encouraged to be treated) like a badge of honour gained in service to their community, so it was less "I cut myself fixing that roof, I should have just stayed moping in the alley" and more "I cut myself fixing that roof, a family is protected from the rain because of me." They would still go Hoen, but at least they would feel like they accomplished something and their injuries reflected their hard work and dedication, rather than a random assortment of meaningless bumps and bruises. Raoden probably figured it was worth the tradeoff.

(Includes Major Spoilers) Shouldn't the chasm line be inside Elantris?
If you look at the map at the start of the book you can see that the Chasm stretches (more or less) from Lake Alonoe to the edge of the Atad Mountains. The chasm line in the base Aon should therefore stretch between the dot in the center to the middle of the curved line on the right, each Aon is built up from this including Aon Rao which the city of Elantris is shaped like. The only parts of the complex that fit the base Aon are the walls of the city itself, the North wall is the coast line and the East wall is the Atad Mountain line, therefor the chasm line should run from the center of Elantris to the Eastern wall. The four surrounding cities are the embelishments that make Elantris into Aon Rao yet Raoden draws the chasm line somewhere between Kae and Elantris. Obviously from a plot point he could not have made the line in the city because A) all the buildings would be in the way and B) the enemy army was also there (busily making a bonfire). Even so this is where the chasm line has to be for the Aon to work (otherwise the Chasm would be on the other side of the mountains in Fjorden).
 * This bothered me too. Raoden is described several times as drawing "the chasm line" as a finishing point to Aons, as if the line is singular when in fact judging from several of the Aons there should be two or three or ten of them (the basic Aon is repeated a lot in some of the more intricate designs.) So maybe the Chasm Line isn't really a fixed part of the central Aon, it just has to be there somewhere as a representation of the crack's existence.

Calculating the distance and direction to the Teod docks using paces and seon is surely beyond the scope of credibility
No-one, not even a mathematical savant, could measure the distance of a sea voyage through paces and even if they could it would not be possible to measure one pace accurately enough to multiply it by 1,327,042 without a huge margin of error and even then it's not taking into consideration the curvature of the planet. Getting the direction correct is nearly as bad even with a magical Seon sense of direction, the margin for error would still be pretty massive even if the distance between Raoden and Ashe were increased to it's visual limits. All in all Raoden would have been lucky not to end up about a mile in the air above a fifty mile radius of Teod. Would have been a lot more convincing if Adien had calculated distance from a much larger eastablished length than his own steps (eg the specific length of a certain road or some such).
 * Reminds me of the character of Brutha in Terry Pratchet's Small Gods. His memory is so perfect he could walk backwards through every step he has ever made in his life but as soon as he gets on a boat he is ill simply from being unable to feel where he is as he floats. Just having been somewhere could not allow anyone to calculate distance in paces if sea travel (or flying) is involved.
 * The kid's pretty obviously some kind of magic savant, though. Presumably he can "feel" the correct number needed through some sort of connection to the Dor. His stride length was a useful benchmark and easy enough for Raoden to draw into the Aon, and then whatever crazy magic Adien channeled told him the correct number to deposit Raoden where he wanted to go.

Who built Elantris?

 * As far as I can figure, Aondor must have had practicioners before Elantris was built, but they were nowhere near as powerful. Then one (or several) of them built Elantris as a massive Aon, which amplified their power unbelievably. However, much like Sauron's one ring, they put so much of themselves into it that it became not just a source of power, but a serious vulnerability. When the chasm appeared, they weren't just reduced to their previous power, but instead were turned into something fundamentally broken. Does this sound right?
 * That was my general understanding as well- when the early Aon Dor pracitioners built Elantris, by making it a giant Aon they in some ways altered the nature of the power they used (not the Dor itself, neccessarily, so much as the way it interacts with the physical world) to make it more accessible. When the chasm altered the landscape and rendered the aons inaccurate, the result let only a tiny trickle of the Dor in- enough to begin the transformation but not enough to finish it, and to suddenly cut off 99% of the power of the existing Elantrians, resulting in the zombie-like creatures the Elantrians became.