I have the same issue with a Birdshead New Vaquero (3.75'' barrel) I bought brand new in January.
Shoots to the left, and if you look down the sights the front sight appears to be tilting to the right. I showed the gun to a lot of friends here, and let some of them shoot it. Everyone had the same impression and similar results with target practice.
I understand two inches of windage is not a big deal, but I couldn't help but being irritated by that. While shooting this gun I ended guessing and thinking about how much mental adjustment to make instead of concentrating on improving my technique.
In my limited experience, most fixed sight single action guns shoot low if you aim at 6 o'clock like you're supposed to. However, somehow I found elevation problem easier to adjust mentally. I usually aim at 12 o'clock with my other .45 LC Vaquero (old model 5.5'' barrel) and it hits dead center. Aiming higher than 6 o'clock doesn't bother me, I even set my adjustable sights Rugers to shoot a little higher than factory settings - all to satisfactory results.
I called Ruger, and they told me to ship the Birdshead back to them with a letter of explanation. The guy sounded friendly, but I got the impression they get a lot of similar complaint from inexperienced shooters. He said something about shooting low and left being a common problem. I thought it would be better to send them a sample target.
Yesterday I took the gun to the range. I was shooting off-hand from 10 yards out, which is closer than my usual distance with short barreled single actions.
First shot I aimed at the right edge of the paper. It hit at the edge of the largest circle right at 3 o'clock. That's two inches.
Then I aimed at the hole and fired three shots. They hit exactly two inches to the left toward the center, touching the black and making a rugged hole, Aiming at that hole I was finally able to hit the bullseye.
The next shot aimed at the bullseye landed once again two inches to the left. I thought the pattern was obvious.
Later last night I packed the gun, put my target in the box and took it to FedEx.
My question is, will they be willing/able to fix it, and was it worth my spending a hundred dollars to ship it?
The Ruger guy said I had to pay for the shipping to them, but they will pay for the return.