When you cut the stock (and I would second Mike's advice), your cheek will be further forward on the stock and therefore higher up. This will raise the point of aim (or point of impact really).

In short it will change a number of effective dimensions on the stock. It may shoot better for you. Or, you may need to file down the comb slightly. My experience has been that comb height and cast are the key dimensions that make the gun shoot where I look, so that's what i would pay most attention to..