I recommend that you bench test the gun at 10 yards on paper. Try as many load varriations, with powder and slug whts as different as you can afford to buy, beg or borrow.
If you have a favorite load, and want the gun to shoot it POA, then stick with load and have the gun modified by Ruger, or by a local GS.
If you want to file after hitting on a favorite load. I recommend a bench, shoot 5 rounds, file a sliver off shoot 5 more rounds, see how it groups and file a sliver off if need be, take only 001. off at a time.
I also recommend that you let another experienced shooter try the gun before going to the trouble of sending the gun off or filing. If it still shoots low then move on to the next level.
If you are shooting Store bought rounds, let Rugger or your GS know the vital stats or give the GS some of the Rounds to work with. I do not know if you can send ammo in the mail or UPS, but you definately can not send them together with the Gun.
BTW, Ruger recommends lining up the sights with the lower part of the bullseye when shooting. Might try the center or high on the B'eye to see how it shoots. As I tell the folks I teach with rugers, put the blade dead center of the camels back and complete the hump, so it all looks like it goes together on the RV's,
Once your sighted in on paper to POA. Try with out the bench. You should be doing well. Just take it slow if you do it your self, shoot 5 at a time to get a grouping (at 10 yards it should not be hard to get a nice tight group off the bench, say 2 to 3 inches). Mark the first 5 shoots with a marker so you can tell or change targets with each batch. Just take it slow, plan on an afternoon of fine tunning your RV. It took me 35 rounds and 2.5 hours to get my AWA, peace maker to shoot POA, with my pet loads.
Vaya Con Dios