Molly, I have encountered this problem several times in my building career (over 400 guns). I do sight in and regulate the sights of each and every gun. I regulate the sights to so the gun hits a smidge low on the target at 50 yds. This allows the owner to file a bit off the top of the front sight to achieve the sight picture they like. Shooting the gun also allows me to test general function, and tune the gun a needed.
Occasional I have encountered a bent barrel and a little tweek fixed the problem. I believe that your gun only needs a little straightening. I once encountered a barrel that I needed to bend to the point of being visable once it was inserted back into the stock. The barrel shot significantly to the right, but after bending it shot great groups, but the bend was unsightly. I ended up sectioning the barrel and found that the bore had wandered off in the center of the barrel. I sent photos to the manufacturer and they replaced the barrel. I took a new barrel out of my stock and replaced the barrel on the build, no more problems. I firmly believe no builder should deliver a gun in "unfired" condition. Everything can look beautiful and work well, but until you put it on the bags and shoot it, you are only guessing...
Ron