Actually the pains you describe can have a very adverse effect on accuracy. Anything that alters the way you hold, squeeze, or address a rifle can change what happens down range. So you did well to over come all of this.

I was talking about rifle address with a friend of mine who shoot competition rifles in tournaments. Also I noticed the stock of his competition rifle had aslight indent right where my cheek met the stock. Nothing major mind you. But I could notice it. He said, did you ever notice how the tournament shooters set their cheek to a rifle and a lot of times will kind of rub around on it. He said, they are looking for that special spot. Of course over time and practice, it starts to become more natural he said. Hethen told me a trick for maintaining head position when you address the rifle. Normally you can do this yourself, but two people make it easier.

Set the rifle in the shooting bench and actually hunker down and get comfortable, just like you were going to shoot. Have the scope or sights the way you want them, and your eyes relaxed, never squint like some people do. Make sure of your grip, etc. Then mark, or have someone mark where the center of your cheek meets the stock of the rifle. At this point, place a simple band-aid on the stock of the rifle. Then every time you shoot that rifle, make sure the center of your cheek feels that band-aid in the same spot. Match the grip and you will notice that when you look over the sights or through the scope, everything seems perfect.

Try that next time and see what happens to your groups.