It is just as I suspected. Your problem is not in the holes for the scope bases, but rather in the timing of the barrel.
Contrary to what most might think, rifle barrels are not straight. They all tend to have some runout in them, even the expensive ones. It just so happens that the bend in your barrel is pointed to the right. To exaggerate things to the extreme, think of a banana. You want the end of the banana pointed up in this case so that you get the most elevation and don't lose windage adjustment. Rifle barrels need to be chambered concentric with the bore and crowned concentric with the bore for best accuracy. They need to be timed to avoid the problem you are having. If you are a little confused at this point, don't feel bad. I was too until I barreled my first rifle and saw the muzzle flopping around in the back of the headstock. Basically, the ends of the barrel are the most important. We want it to go in straight and come out straight. The middle of the barrel is just a pipe.
What needs to happen here is that the barrel is removed and the shoulder set back until the barrel lines up at top dead center with the centerline of the receiver. The shoulder will probably need to be set back about .045" (this part can get a little nerve wracking). Unfortunately, all of the lettering on the barrel is not going to be lined up anymore. Your gunsmith will also have to set the chamber back, but that is not a bad thing.
It sounds like you have a good barrel. Once it is timed, you will be a happy camper (other than the lettering).
Clear as mud?