If you do the joining of the points manually, you can probably do a much better job of reconstructing the object. Otherwise, you are likely to end up with a bunch of splines or a mesh to mess with, and most likely you would end up wanting to straighten up and simplify the model anyways.
I like the idea of the 3 axis linear scale idea, in some kind of gantry setup, guided by hand. However, in real life, I wonder if a person would find it too tedious to do?
I wonder what the users' working impressions are, who have used a Microscribe or Faroarm digitiser?