I actually would use the rifle sights to test. Shoot from a rest at 25 yards with the rifle sights at their lowest setting. Shoot 3 rifle shots at a a spot in the center of the patterning paper, then carefully aim a couple of shot loads at the same point. If they coincide, then the barrels, rib and sight plane are roughly consistent. If the shotgun barrels are shooting much higher than the rifle, then your rifle barrel and shotgun barrels aren't regulated vertically. There is a lot of infoo and discussion about double rifle regulation, but strangely enough I have never seen a discussion of drilling regulation, which should be a similar issue.
