Applejack and Rainbow Dash should have more Stamina than Sanity.
Fluttershy and Rarity strikes me like the other way around.
Twilight and Pinkie should be 50/50.
But that's just my gut reaction.
As for abilities:
Pinkie should reduce Sanity loss by 1, with all her singing away the fear. Or maybe give back Sanity like the phsychologist.
Fluttershy should have "The Stare", reducing/re-rolling rolls to sneak past (or in this case, make them back down and go away).
Twilight should really have an affinity for magic, lower cost or more "hands" or starting with more spells or somesuch.
I'll be back for more ideas, if I get them