Cardsplitter: The LAST thing you do is file on the muzzles. You asked how this was done, and I told you. I did not tell you to start doing this after the first shooting of the gun.
First you do load development. Get a good pattern, or, if you are going to shoot only RB, then test EACH barrel for the most accurate load. Sometimes using more or less powder will raise and lower the POI. As to windage problems, remember that the stock is your rear sight, as your cheek, fitting against the comb of the stock determines how the eye sees that front bead.
If I owned a guy that was shooting only a couple of inches to one side or another, I would consider two fixes:
1. Simply install a rear sight, or mark the tang with some kind of line that would bring the bead over enough to move the POI those few inches.
2. Consider having Cast Off put on the stock, by having the stock either bent, or if its a half stock, a little filing in the stock mortise at the back of the action( you file the wood, not the metal) to bend the stock would work. I did this with a Remington Model 870 shotgun to give me "Cast On" as I am left handed. The gun now mounts and shoots very well for me.
If a POI is high or low, I would consider filing down the comb to lower the POI, or adding wood to the comb to raise the POI. Shootes use " moleskin " or various kinds of cloth, incuding terry cloth used in towels and wash cloths, as someone else has suggested to raise the comb while testing. I have seen duct tape, cardboard, and all other manners of temporary additions to the comb to raise the POI on shotguns, until the correct height is achieved. Then, something more permanent is installed or a new stock is cut to the correct dimension. Again, I have seen extra wood added to the comb, by cutting a flat on the top of the stock, and epoxying a new piece of wood, which then is filed down to the correct dimension. This is such a common need for shotguns that some of the more expensive breech loading shotguns come with an adjustable comb. That kind of stock would be perfect for someone intent on shooting RB only.
Now, I have restricted these comments to shooting RB only because most shotgun barrels are NOT designed to shoot round balls: instead, they are designed to shoot shot loads. The barrel walls are thin, to lighten the weight of the gun, particularly in DB shotguns. Light barrels tend to have wildly different harmonics, and they tend to shoot away from each other, at least with shot loads. What a give set of barrels will do shooting Round Balls is anybody's guess.
The reason I now have a fowler is because the back half of the barrel is a strong octagon design, and the round front half is at least twice as thick as the barrels on my DB shotgun. Its far less tempermental shooting round balls than my DB shot gun, with its thinner, round barrels.
Now if you are going to shoot Shot loads out of that gun, too, then you need to decide what is going to be the gun's primary use, or function, and work up loads. If you have to move a pattern because its striking center a foot or more away from POA, then its much more important to work on that situation with changes to both the stock and barrel, than moving either for a 2 inch variance shooting round ball. You don't give the range, but if a shotgun is putting a RB within two inches of POA at 50 yds, You can't hold the sights on a live target tight enough to notice the difference. And remember, you are hitting that deer with a massive projectile, that weighs over an ounce, and will expand on impact to cause a massive primary wound channel.
For a 2 inch drop in POI, I would try first increasing the powder charge and add a good OP wad to my load to see if my POI would not raise. Then, and only then, if nothing happened, I would add material to the comb. Finally, if that just didn't do it, I would consider filing down that front bead some. It would not take much to move the POI 2 inches higher.
The last thing I would do is file on the muzzle. I would however, begin all this by checking the muzzles to see that they were cut square to the Bores of the two barrels. I would want to know that the crowns are correct, before filing any on the stock or the muzzle, or the sights.
