I've done what you suggest as a solution to centering your impact points. It worked for me, but was a royal PITA. Two inches is a lot to take out of the rear sight, and believe me, bending the front sight is
NOT AN OPTION. Were it me, I'd
send it back to Ruger and have them screw the barrel in the proper position.
As to which side of the sight to, file...if your groups are impacting 2-3" right of your point of aim, file the rear notch on the left side. I did it with a NV in .45 Colt as was able to get almost 2" of lateral movement, but that was about the limit, without a noticeable widening of the notch, making precision sighting at 25 yds, problematic.
In practice, I shot a lot of groups with my standard load to determine, just how much adjustment was necessary. I shoot 95% of the time with two hands, so that's how I zeroed the gun. Since my one-handed and two-handed zeros are about 2" apart in lateral, (windage) adjustment, I needed to make that decision. I'm a rightie, so my one-handed zero is another two inches farther left from my two-handed zero.
Shoot a lot of groups, and not off the rest...shoot them as you'll shoot in the field and when plinking, then determine just how far out they are; and zero for that amount. Guns shoot differently off sand bags than they do offhand. It's a matter of the way you hold the gun, amount of downward pressure on the sand bags, arm support, the amount of sight you're seeing, and hand grip strength.... all have a profound effect on group location...hence my suggestion that you shoot a lot of groups as you do in the field. Then and only then, get out your file, mask the rear end of the frame with electrician's tape and begin. It's file two or three strokes, then shoot a few groups. Then back to the file again...and with the load that you're committed to for the rest of the time you own that gun!
Here's a pic of the rear of my Vaquero, if you look closely, you'll see the widening on the right side of the notch.
Hope this helps. But a call to Ruger is really the best solution.
Rod