Did you try the stock shell to see if it appears parallel when inserted? That may be the only way to judge if the arm is off. This is a tough one to comment on otherwise because I haven't used your head shell. I assume the Ortofon shell has a flat top to aide in this evaluation.
I also am using aftermarket head shells with my 1200G. I never did try the stock head shell to see if it appears parallel in the arm but given the quality of the entire table I'd be surprised if the arm is off. I got 2 identical LP Gear Zupreme head shells for cart swapping. The Zupreme does have azimuth adjustments and I found I had to take advantage of that. The azimuth was pretty far off on both when I first put them in.