Fairly sure I already know the answer to this, but would the damage from a Sanctified weapon rune stack with the damage from an elemental rune? I'm pretty sure the stacking rules would prohibit it, but I couldn't find it in the FAQ document.

It is the same type of bonus (a static number) from the same source so no they would not stack (which is why I didn't take the spell which grants them for my character)

Thanks, figured as much.

Yep. A bunch of people get screwed by stacking with Sanctified Weapon. Others get less screwed by needing to boost the rune to exceptional to get any effect. There are a few deity spells that I think need to be revisited (Fire Dragon seems to be consistently at the short end of these spells).