What kind of equipment do you have available?
The first thing we would do in the shop would be to mount up the receiver in the mill and check the alignment. We usually drill out factory screw holes for one size bigger anyways, so that we can gaurantee the alignment.
In a "other" case scenario, a bench vise and you can use a set of dial calipers to compare the measurements front and back.
In a worst case, you can take your basic measurements and see where the holes stand.
Now, another option is to mount up a one piece rail and hand lap the scope mounts, but then you are getting into a territory where you need to do it right, or you are going to end up making things worse.
What have you got to work with?