Ok, have read all the threads. Some totally amazing points and catches by people here. Really makes me respect the layering and thought that PR put into these books. Sad that he doesn't seem to ever put a real climax into the books.

I'm assuming this problem will go away in the third book, which will naturally have a climax.
A couple of random thoughts from things said in the thread.
1) I don't think there's evidence to say that Master Lorren knows who Kvothe's mother is. I think that Kvothe's father having approached Lorren in the past about knowledge of the Chandrian is a natural explanation for the reaction. There's no reason to think that the
name of the Ruh that ran way with Natilia Lackless made its way in story form all the way to the University, even if the story that she ran away with troupers did.
2) It would be a great twist if Bredon/Ash turned out to be an Amyr.
3) The Ch-fae tree guy seems to have sent Kvothe firmly down the path of opening the Lackless door, which I agree with others is going to turn out to be a very bad thing for the world.
4) SSE, great idea about Shaping = Sympathy, but I agree with others that it is not right. I haven't seen someone point this out yet, but I think Shaping is the "lost art" that created the things that Kilvin tells Kvothe about: the old sword, the force-field wall, the everburning lamp, etc. My hunch says that shaping created the Scrael as well.
5) Do not for one second buy that a scrael is in the Lockless Box. That doesn't make sense to me. I'm guessing it has to do with the Lockless Door, but the present day Lackless have lost the info. Likely it will be some sort of ball shaped object(s) to make the song correct.
6) I'm still confused about the Creation War. So Namers and Shapers are all like "this world isn't big enough for both of us". And Iax ends up creating Fae for the shapers to live there. And then he steals the moon (on a part-time basis). So the Namers are all "oh it's on like Donkey Kong now!" And they fight. And the 7 cities of Namers have the upper hand. But then Lanre gets all mad that Lyra dies. So he corrupts 6 of 7 people in the 7 cities. And they become the Chandrian. And (somehow) the Creation War ends in a stalemate with one Namer city left and the Shapers trapped in Fae with the Greystones. Is that basically right? Was Lanre pro-Shaper at the end or anti-everything? Are the Shapers the big-big bad or just misunderstood?
That's about all I can think to add to this discussion, which has been one of the best discussion threads for a book on this forum ever. Great catches everyone.