I'm certain that trying to mate the differing profile of the repro sub rail to the original would be problematic at best, and may even lead to body alignment issues.
It seems to me that using a matched pair of the repros might be a better idea - if they aren't too different from the original. Do you have the chance to compare them side by side to see if the general shape and some of the key points on the rails will match up?
I've seen photos posted here on the Barn from guys that have built their coupe bodies from the sub rails on up. I don't recall if they were using originals or repros, but maybe they will add further comment.
Good luck, let us know what you find out.