"Red and Black" by storyless, starting with flashbacks to the younger days of our heroes. Chapter 2 just posted: young Auron.
"Necromantia" by TrekQueen, tracing the relationship between the pair on Yuna's pilgrimage, starting with their first meeting at Luca. Chapter 1.
Both may be found on Ficwad. They are rated NC-17 for expected mature-content in future chapters (Red and Black has some R stuff.)