Forgive me jumping in (and apologies if I've missed something) but is the geometry of the measuring setup ideal? As mentioned, the measurements are dependent both on the straightness of the rail and of the beam itself and it's not really possible to separate out the two. If you turned the sensor through 90deg so that it looked along a line parallel to the gantry, and placed the line source just off the end of the gantry but with the laser line intersecting the sensor, you would then be moving the target down the length of the beam (straight apart from gravitational bending!) rather than relying on the optical quality of the cylindrical lens generating an accurately straight line. However, you would need to get the laser line horizontal to reasonably close limits both on the roll and pitch axes (if that makes sense).

When I first started following this thread I had a picture in my mind of a point laser shooting a beam parallel to the rail being measured and striking the sensor in the middle. What I have described above is really only the same thing but using a line source to make lateral alignment less critical.

Or I might have missed the point but I do find this whole exercise very interesting to follow.