Speculative more detailed map (click blog post title to view). Most locations are directly from here: http://www.tor.com/blogs/2011/08/rothfuss-reread-speculative-summary-part-1-qinside-edges-holesq-speculations-on-imaginary-geography so please read (or at least skim) it before saying I'm wrong outright. =)
The old cities are mentioned in Skarpi's story - in ch 26, Lanre's Betrayal:
"But eight cities remained. They were Belen, Antus, Vaeret, Tinusa, Emlen, and the twin cities of Murilla and Murella. Last was Myr Tariniel, greatest of them all and the only one unscarred by the long centuries of war. It was protected by the mountains and brave soldiers. But the true cause of Myr Tariniel’s peace was Selitos. Using the power of his sight he kept watch over the mountain passes leading to his beloved city. His rooms were in the city’s highest towers so he could see any attack long before it came to be a threat."
Imre/University area is definitely Belen. This is how Denna's note to Kvothe is addressed:
Kvothe -- Anker's Inn. University. (Two miles west of Imre.) Belenay-Barren Central Commonwealth
The Great Stone Road goes into the mountains in the book's map, so it would make sense to have it end at Myr Tyriniel, especially considering the above quote from NotW about being protected by the mountains.
Tinuë is actually one of the only cities that exists on the original map inside the KKC books, so it is real. When Selitos describes the one city that survives after Lanre betrays them all, it's close enough that he could see it from Myr Tyriniel. Considering where Myr Tyriniel is placed, Tinuë is the only one that it could be. And since Tinuë has become a colloquialism in the Four Corners, it would make sense that it was the one city that wasn't completely betrayed. The one that lasts through history and becomes a common saying.
Myr Tyriniel is also shown at the edge of the Old Stone Road because of Arliden's poem about "something something ell" and I've placed Tinusa as Tinue both because of the name similarities, and if Selitos could see one city survive from his city of Myr Tyriniel, it would have to be close.
I put Murilla and Murella as the city of Renere, which is called the "three part city". (Pat says Kvothe will go there in D3, here: http://goo.gl/cZ7knA) It was conceivable that the ruins of two old cities could have two new cities built on top of them, and when they grew enough, they combined together to have the part between the two cities be the third part of the three-part city. I put the twin cities as Renere because of this : "It was confirmed by Patrick Rothfuss that Kvothe will visit the capital in the third book, named for now 'The Doors of Stone'. In this same interview Rothfuss called it 'the three part city'."
Antus (Atur) and Emelen (Anilin) were placed because of the similar sounds of their names between old and current cities, which seemed to make the most sense.
And for Vaeret, I forget, but I think I placed that one there because of how balanced it felt on the map to put that one there (it didn't really fit anywhere else) and Kvothe mentions something in WMF about the Eld being able to swallow entire cities and no one would notice.
And the location of Newarre and, to an extent, Severen, are largely from the research here: http://www.tor.com/blogs/2011/08/rothfuss-reread-speculative-summary-part-1-qinside-edges-holesq-speculations-on-imaginary-geography
Anyway, thoughts appreciated :)