1) About the direwolves, I assume that, like in RL, a direwolf's main source of food is the larger animals (elk and such) that grey wolves can't catch as easily. The only place we see the really large animals, too, are beyond the Wall. Is this why direwolves live almost exclusively beyond the Wall, or is there something I'm missing?
There are large animals south of the Wall as well, especially in the wolfswood, the kingswood, and the rainwood, the three largest forests in the south. But I suspect that direwolves fled the advent of man, or were hunted out... they are far more dangerous to humans than ordinary wolves.
2) I'm also curious about the religion of the Seven. They seem to be (superficially, at least) an analogue to the Catholic Church, but the Great Sept is in modern times simply the mouthpiece of whoever's in power. Before Aegon unified the Seven Kingdoms, did they enjoy more of a powerbroker?
Generally yes... although (as with the Catholic Church), the Faith's power depending in great part on who was chosen as High Septon. Even Aegon tred lightly where the Faith was concerned... it was his son Maegor who broke their power, but even then the Faith came back under kings like Baelor the Blessed.