The problem is likely to be getting a consistent strike/attack. How you hold it, how you press down the strings, how you pick/strum, all impact the sound. I would rig up some sort of mechanical striker to generate a consistent attack/pluck/whatever and ensure it is placed at the same place on each guitar. Failing that, I would use a pick on an open string or use a capo (to avoid differences from finger fretting), and strive for the same measured amplitude as well as consistent speed of attack.
I have a vague memory of doing this ages ago back when I was building effects boxes and was curious. IIRC I modify a rat trap (bigger version of a mouse trap) by stopping or replacing the spring (too much force as-is) and putting a little rubber foot on the trap bar (cut a slot in the foot and glued it down with a small square of wood). I added wood strips and clamps to attach it securely to the neck, then used a string to trip it. I think I extended the part that the spring attached so it stood an inch or two higher than the bottom plate so it could fit around the neck. It's hard to describe but was not too hard to make and use.