Here's my humble input:
I am (was) a part-time luthier, using CNC to do my parts.
Best approach is to do a full reverse engineering process, and go section by section.
Rebuild contour, headstock, neck profile sections (1st fret, 12th, heel) etc etc.
The real plus side, is that you can do each section of your neck parametric, and link a CATProcess to it.
I had it configured like that, basicaly you edit a profile section (say you want a Fender Eric Clapton V-shape neck).
So, edit profile, update model. Update process. Output APT. Post-process, and get G-Code. CNC machine.
Same applie to scale length, width at nut, heel...you could even configure patterns in catia to have 6, 7, and 8 string models that would uptade automaticaly.
Rinse and repeat.