I like a lot of this, it mirrors much of my own thinking.
Where my tinfoil theories diverge, however, is that I think that when Fen'harel sealed away the remaining pantheon he found a way to separate out 2 parts of their soul -- the dragon aspect and the 'normal' elven bit. That separation was intended to cure them of the taint and stop their warring, but in fact it robbed them of most of their magical ability, and probably left them mere shadows of their former selves. So he had to think on his feet, and to buy himself some time he sealed them away separately, the elven parts in the fade somewhere, and the dragon aspect - which was still corporeal - down in the abyss/void/underground/whatever you want to call it.
These dragon aspects were of course tainted, and as super powerful and huge loci of the taint darkspawn are drawn to them. Everyone in Thedas has it wrong, of course: when the darkspawn reach them they don't taint them and cause a blight, because they're already tainted -- they merely set them free. These dragons then go rampaging across Thedas fuelled by a blind rage for a war they can't even remember any more (since they're not whole).
This is also why Solas is so grumpy with the Grey Wardens. They're slowly killing the dragon aspects, meaning he and Flemeth have no chance to reunite the 2 halves for most of the pantheon now (also explains why Flemmy wanted the old god soul free of the taint - I wonder which god's soul that was). But beyond that, the Wardens think killing all the old gods will stop blights and eventually end the taint, but really all that will happen is the darkspawn will no longer be drawn to the next huge loci of the taint (keeping them largely below ground when there isn't a blight) and will instead just roam around aimlessly - a perma-blight of sorts. Whether that would be easier or more difficult to contain I can't say, but Solas mentions his doubt about the death of the old gods meaning the end of the troubles in dialogue at some point. I think this is why.
I agree Arlathan is the Black City. I expect it was once the seat of Elgar'nan. Each of the gods had their own temple and around it a city, and it makes sense that the largest and most beautiful of these was for the head of the pantheon. He was also the sun god, so perhaps it was gilt - a Golden City. The fade apparently reflects what people expect to see, what is in their dreams and memories, so if this beautiful Golden City was the most impressive and seat of the most powerful elven ruler/mage/god/thing it makes sense it would be present in the fade in some way. Over time, and after the death of the elves, it got reinterpreted in various ways, eventually being interpreted as the seat of the Maker. Fen'harel had, of course, in the meantime sealed the real Arlathan away, in its blackened, corrupted form, and when Corysplat et al happened across it in its physical form they - and the rest of Thedas - did the only thing that they could logically do: they interpreted it as the Golden City of the Maker turned black.
I don't completely buy into that theory that Sera is Andruil, but it's heaps of fun so what the heck: since my theory relies on a certain concept of duality with regard to the elven gods' souls/beings, perhaps their being sealed away relied on that as well. If Andruil's dragon aspect has been slain in one of the blights, perhaps her elven remnants of soul became destabilised from their prison in the fade, and were drawn back through to the mortal plane. If so, it's possible she's in Sera, and it would explain this preternatural skill she has for using a bow that she doesn't really understand, and all the little things Cole and Solas say about her affinity for the fade, and for her abject fear of going into the fade. She doesn't know who she is, but there's something buried there. She can never be whole again, at any rate.
I'd go further if we're going down this crazy line of thought, and say we can say the same of Sandal, possibly having the remnants of June, which is why he has this strange connection to the fade, but doesn't know why.
As to why we'd necessarily end up encountering all these bits of elven gods... I guess it's not outside the realm of possibility that something hidden in them causes them to try to seek out important events in history. I'm reaching. But it's fun to reach!
As for the forgotten ones, well I think they are just another way of describing the pantheon when they were in their dragon form. I think the reason the whole warring kicked off was differences of opinion over the use of the dragon form, over abuses of power, etc. Andruil's mosaic says she used to go down into the void to hunt the forgotten ones. I think this was her starting a war against the way the pantheon was abusing its power. That she ended up bringing the taint back with her was rather unfortunate, and escalated it to a point none of them probably envisaged. We know that a disciple of Dirthamen's was punished by Elgar'nan because he wanted to have the dragon form as well, but it was reserved for the gods and considered sacred. We know that abuses of power were rife because they used slaves. The mosaics paint pictures of a pantheon very different and far more dark and violent than the ones we'd come to understand through Dalish mythology. As to why they were called the forgotten ones while in their dragon form I don't know. It depends, I suppose, on when these mosaics were created. Were they created when the gods were still alive, or afterwards? I know the temple dates from when Mythal was still around, but it could have been added to by the sentinels over time as they sought to retain as much history as possible. Well we know what time does to history - the whole series has taught us that it gets warped and twisted into something different.
My ideas have changed somewhat, and originally I thought the forgotten ones and the pantheon were two ideologically different sides of the same ruling class, and they warred as a result of that (and that the forgotten ones were in that case the old gods). But the numbers match so wonderfully, and the stuff about duality can explain so much, that I've largely abandoned that idea.