<a href='http://www.fanfiction.net/s/6763234/1/Herwald_von_Einzbern_and_the_Philosophers_Stone' target='_blank' rel='nofollow'>"Herwald von Einzbern and the Philosopher's Stone"</a> is the story you may be looking for. This is Harry Potter if he'd been adopted by Emiya Kiritsugu and then the Einzberns subsequently. He was involved in the Grail war as the master of Assassin, most probably Jack the Ripper. The story also cameos Hoenheim and Trisha Elric as Mr. and Mrs. Flamel. Oh, and the Einzbern's specialty, alchemy, plays a major role. Herwald has Scar's alchemical arrays.
On another note, I'd like to see a Harry that received a visit earlier in his life and an offer to go to boarding school in America on a scholarship. The school is Xavier's School for Gifted Youth. Harry is a Mutant. And his power...is Love. He can make a person or people in a certain proximity feel love, joy, and affection. Yes, he has a Care Bear Stare. Given the emotional nature of most magic, that makes him a nightmare to duel. He also has combat training. Oh, and his guardian for his stay at the school, a recently reformed Professor Erik Lensherr (AKA Magneto). I'd love to see what Magneto would have to say about Voldemort. Hell, I'd love to see any Legilmens try to get into Harry's or Magneto's head. Charles notices the intrusion later on and pokes the intruder with a comment, "How cute, you think you can read minds."