Not sure if it's accurate, but the wiki's Ages section says Arlathan was destroyed in 220 TE with a horrifying blood ritual and the first Blight began in 800 TE. The ritual they performed to physically enter the Fade used the blood of hundreds of slaves and 2/3 of the lyrium in the entire empire. After the visions the Warden had and the quest line into the Deep Roads, I figured the city Tamlen saw was Bownammar. The elves could also use the eluvians for transportation, as well as communication. The Tevinter magisters however, could only figure out how to use them for communication. Corypheus said the city was black when they got there. It also seems to indicate the Maker was not there.
"The city! It was supposed to be golden! It was supposed to be ours!"
"The light. We sought the golden light. You offered... the power of the gods themselves. But it was... black... corrupt. Darkness... ever since. How long?"
Also the Forbidden Ones (Xebenkeck the Undying, Imshael, Gaxkang the Unbound and the Formless One) were the ones that taught the magisters blood magic.
"The blood feeds, the blood nourishes. In blood, the call is heard. In blood, the deal is made. My master bathed in a river of blood, Then the Great Xebenkeck came!" ―Dabbon Hait
"The first of the magus cast themselves deep in the Fade in search of answers and power, always power. They found the forbidden ones- Xebenkeck, Imshael, Gaxkang the Unbound, and The Formless One. Many conversations were had and much of the fabric of the world revealed. And thus the magic of blood was born." ―Unknown Mage
Flemeth being the Maker or Fen'Harel wouldn't surprise me, I've had several theories involving those ideas. Also that she could be the spirit of Toth via OGB methods. Anon, she is definitely not just a powerful witch. At least a couple characters state that she is no mage or abomination, she's not even human. She's at least 600 years old for starters.
And the eluvians aren't tainted because they they are connected to the Fade, they never really say why they are tainted but presumably simply because darkspawn used them and they taint everything they touch. They may have been using them since the Tevinter magisters that first turned into darkspawn, who would have known about them. In any case, the Black City seems sealed off from the rest of the Fade somehow and there appears to be no taint anywhere in the rest of the Fade.
I've theorized that the Old Gods were not gods but spirits, among the Maker's first children, becoming the first demons. That they were archdemons long before being tainted. That they tried to conquer the Golden City but corrupted it turning it black and then were cast out to their underground prisons, still untainted. They taught the magisters rituals to unbind them but first they had to find them. The OG/ADs used the magisters lust for power in an attempt to free themselves that failed miserably.
First with the eluvians, when the magisters couldn't figure out how to use them for transportation, then with invading the Black City, which they sent the magisters to either in a search for answers or as punishment. When they arrived, their own darkness combined with the darkness in the Black City, creating the taint and turning them into darkspawn. They returned with the song to guide them and eventually (possibly not even until recently) figured out how to use the eluvians. Once the darkspawn find the OG/ADs, they awaken them, but taint them.
They discover that this taint traps them in the mortal realm and use the Wardens to kill their earthly bodies so they can return to the Fade. The Wardens say they are destroyed, possibly even believing it themselves. Maybe the OG/ADs even somehow take the now vacant Black City. OGBs possibly being a way to keep at least 1 trapped here. --Vampire Damian