The first is Marissa and the Wizards, by JCCollier. JC has only posted this on Mugglenet Fan Fiction, to my knowledge, so you might not have seen it before.
If you liked Alexandra Quick, or Hogwarts Houses Divided, I am sure you'll like Marissa and the Wizards. Marissa is a homeless girl living on the streets of Sao Paulo, Brazil, when she receives an invitation to attend Witness Stone school. So, it's another cast of OCs in an original setting -- Brazil in this case. In addition to all the adventures you'd expect as a Muggle-born homeless girl discovers magic and makes friends and enemies at her new school, there is a larger crisis threatening the entire wizarding world.
Marissa's story is sad, funny, imaginative, and touching. The author has created an original Brazilian wizarding world at least as detailed as my American one.
The only negative is that it's a WIP, and JCCollier writes very long chapters, very slowly. Yes, it's been over six months since the last update. I've talked to the author, so I'm sure the story hasn't been abandoned, but I'll admit, at this rate I'll probably be writing AQ4 before Marissa and the Wizards is finished. Still, if you all go over there and show JC some review love, maybe s/he'll be motivated to get that next chapter up. :)
The second recommendation is pcharmed86's Briallen Bevin and the Snatcher's Cave, and the sequel, Briallen Bevin and the Clocktower Guard. To be perfectly honest, I can't recommend Briallen Bevin's stories quite as strongly, for two reasons. The first is that although I love Briallen and find her to be quite an engaging heroine, pcharmed86's writing is a bit unpolished. Her American setting is, in my opinion, a little too derivative of Hogwarts, and her story isn't plotted as tightly as it could be. The second, and more serious reason, though, is that I'm pretty sure that it's been abandoned. I emailed the author many months ago, she promised an update was imminent, and then... nothing. It's been almost a year, so I'm not hopeful that book two will ever be finished. Still, I stumbled across this when I was looking for other American wizarding school fics, and it's one of the few that I actually liked, so you might enjoy it as well.