When we did my rail kit we drilled the outer plates at the same time as the angled rails (clamped them together).
As far as where to put the rails, I put mine about 1/4 in below the top of the stringers (just because it looked good) and trimmed the plates to get the motor where it belonged, like you said.
As far as where to put the rails, I put mine about 1/4 in below the top of the stringers (just because it looked good) and trimmed the plates to get the motor where it belonged, like you said.