If I understand you correctly, the ways of the cross slide are not parallel with the bed ways, as determined by theflat portion of the bed ways. It isn't necessary that they be parallel for good lathe operation. In use, you advance the cross slide toward the centerline of the spindle. You could be advancing along vertical path with the same results. It is possible that the lathe never was parallel to start.
The amount of material removal to make it parallel is excessive and could create more problems than it cures. To start, I would blue the way prism to se where the contact points are. If you are achieving contact over the entire prism, chances are good that you don't have the wear that you believe you have.