This story was just found at sgastoryfinders at LJ and it is just such a cool story I had to share. 

Five Pieces of Atlantis that Jim Treasures is by cassiejames over on LJ.  Its a crossover between Star Trek and Stargate Atlantis, told from Bones POV about Kirk and his pieces of Atlantis and conversely his ancestor, John Sheppard.  I loved this story to pieces.