Marcus:
You said that, "...I tend to shoot best with just the toe of the stock on my shoulder..." This statement leads me to believe that you may have solved your own problem. Why? Because when you shoot with just the toe of the stock on your shoulder what you are doing, in effect, is to raise the height of your stock's comb. The result is a higher-shooting gun, and a better overall score at Trap.
As for the brusing of your cheek, your gun may have too much drop at the heel. This can be illustrated as follows: Take your right index finger (assuming that you are right-handed) and lay it level beneath your right cheek-bone. You should feel a fairly broad area of contact between your cheek and finger. Now, keeping your finger straight, begin to angle it downward from the rear. Do you feel the increased pressure on your cheek-bone? This is because you've reduced the area of contact between the fleshy part of your cheek and your finger, and concentrated it on the area just below your cheek-bone where the skin is thin. If this is the case, then you can compensate for this excess heel-drop when you build up the comb using cardboard or moleskin--imagine a wedge-shaped shim (as viewed from the side) with the point toward the action.
As for looking at your gun's bead-sights, don't. Look at the target! As the late Gene Hill once said in his Shotgunner's Notebook: "...a vast number of gunners sight down the barrel instead of looking at the bird. Let me assure you, you can't do both and be a good wingshot. You must ignore the gun and look, and look hard, at the target--and wherever your eyes go, the gun barrel will go all by itself! Doesn't that sound easy? It is and it works."
Please forgive the multiple suggestions, but unfortunately shotgunning problems tend to have multiple causes. I hope that these may work for you and help you to become a better shot.
Good luck, and good shooting!