I actually do think that breaking a gun in can change its point of impact. I had a USP 45 fullsize about 5 years back and the first range session of 250 rounds it was all over the place. I figured it was just me and let some other fellows try it and it was still all over the place. I took it home and cleaned it and scratched my head some. A week later I took it back to the range and it was shooting dead on in tight little groups (by my standards and abilities they were tight).
As regards the SA shooting low - I have heard this a fair amount, and I believe the front sight is a little high on them. Just make sure that when you start filing and fixing that you are using the ammo that you want the gun to be sighted in for. If you sight it in using 230 grain S&B ball and then put 185 grain golden sabers in there for carry you won't be able to glue anymore on the front sight. Also, and this is said with humbleness and the self acknowledgement that I have a long way to go and much to learn - I would put a few more hundred rounds through it before I started filing or fixing anything just to be sure. If you are getting good, tight groups but they are just a little low I wouldn't be too worried as that should be an easy fix with a file.
Let us know what happens. Better yet, send it to Mr. Heinie and have him put a set of straight eight night sights on it with a slightly lower front sight. This seems like a good way to convince the wife of the necessity of the new (better) sights to me.
Good luck brother.
Jake