You need to start over with the rail first, making sure it is flush with the receiver. Then you will have to loosen one of the scope mounts and get both of them flush with the rail. It seems one of your scope mounts isn't solidly in contact with the rail, or the rail itself is not right. Since one of the holes doesn't match the receiver, my bet is that the new 20 moa rail is your problem. My bet is that there is absolutely nothing wrong with the scope at all.
Joe
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