Interesting topic. One which should see a lot more attention.
IMO, the first thing is to get the stock properly adjusted for length of pull (LOP). Most factory stocks come 13 1/2" I'd guess, most people I know have more than that (except for a few ladies). A smith will have to saw off the factory pad, then glue and screw a spacer and Limbsaver to the butt.
Then center the recoil pad on your shoulder, so that neither the top part (heel) or bottom part digs into the shoulder.
Then without scrunching your neck down, or stretching way forward or backwards, the scope should be mounted so that you can see straight through it. (This is one part of getting the NPA -natural point of aim- which is so important in accurate shooting). You will be seeing straight through when there is no black shadow or smudge at any side of the field of view.
Larger objective lenses (from 56mm on up) mounted with a reasonable amount of clearance from a fat barrel should be high enough; for me that's a good height. I don't buy the argument about mounting a scope really 'low' so it's more 'stable'. It's better to keep your neck straight and not stressed. Only if you're mostly prone will the scope be a tad lower.
Then you mount the scope at the proper distance from your eye so that you get the best (largest, clearest) field of view in good daylight (don't confuse that with the focus). In any case you need a minimum of 3 fingers of eye relief from your end of the scope so it doesn't slam into your eyebone.
Then the top of the stock (comb) has to be brought up so that it notches tight underneath your cheekbone, without moving it on your shoulder. (Good trick - the only way I know of to do that is with a spacer or extending the adjustable cam up on the Palma-class stocks).
http://www.savagearms.com/firearms/model/12%20PALMA
That's to always ensure you're always looking though the scope the same way. If the stock is just laying against the side of your cheek, you'll be guessing by feel if you're at the same place you were last time. No good. Nobody can feel that accurately. So you'll be aiming a bit higher or lower (and maybe right to left) every time you shoot without knowing it. The farther the distance the worse it gets.
So, first the LOP, then the scope height, then the eye relief, then the comb height.
Of course there's also a catch. When you get hooked under your cheekbone by the recoil of a medium big bore it's gonna hurt. That's why the Weatherby monte carlo stocks were set up the way the were - to fly away from the cheek on recoil. But they would have to be made high enough to get any sort of good cheek weld. Most I've seen aren't. So dense padding of some kind has to be solidly fixed or manufactured into the rifle stock onto the comb or comb adjustment.