Sorry to be late to join but...
Didn't the OP say he was unable to adjust the point of impact of his rounds "down" to the point of aim of his scope - no matter how far down he adjusted the scope? IOW, that the rifle was shooting too high?
If I am understanding that right, then doesn't that mean the rear base is too high? That makes perfect sense if the radius at the back of the clip loading hump is interfering with the rear Weaver base seating correctly on the rear bridge, and thus sitting too high. Many people are talking about shimming the rear base - wouldn't that make the problem even worse?
If it were mine, and the problem really was the bullets hitting too high with the scope adjusted all the way down, I would carefully file a little bit off the underside of the forward portion of the rear base to see if that would allow it to fully seat on the rear bridge and maybe fix the problem. Only out a few bucks if it doesn't.
Then again maybe I'm missing the OP point but think about what I just wrote and visualize the line of sight and the line of bore.
Best of luck with it,
Rex