Like garmenteros said, string spacing is a big one right off the bat. Things that will simplify the process in my view:
fretboard wood, binding, dots, inlays?
type and colour of tuning machines
volute on the neck or not
tilt back or flat headstock with string trees
type of frets (thickness of wire used)
preferred neck thickness
zero fret or regular nut
number of frets (24?)
truss rod access at nut or body?
neck material (stringers, multi lam, one piece?)
neck through, bolt on, set neck or some combination?
traditional, modern, original design?
solid colour, or visible wood grain or some combination?
number of pickup routs & location
single cutaway, or double cutaway design
depth of cutaway for fret access
location of bridge from edge of body
strap button locations
chambering (is weight a consideration?)
pickup guard or not
type of jack & location on body
bridge type and colour (best if this is known firmly right away)
roundover on edge or not
tummy cut, arm contour?
electronics (passive, active, type, preamps, etc)
If you have this somewhat nailed down, it's a good start for the conversation about details that's to follow...
JC beat me to it. Can you hear his experiential frustration in his typing? LOL!