Mike:

I believe that you should do as the airplane designers normally do: to use the center line of the fuselage as your horizontal reference.
They estimate that this is the attitude that achieves the minimum drag for cruising speed at level flight.
Because the wing AOA changes for slower or faster level flight, the center line of the fuselage will deviate from the horizontal for other than the cruising speed, increasing the total drag of the airplane.

However, the angle of the centerline of the horizontal tail not always coincides with the angle of the centerline of the fuselage.
As you know, the function of the stabilizer is to lift down in order to compensate for the total pitch torque or moment produced by the wing, thrust and drag.
A few airplanes require a positive lift at the tail.

Please see the attached schematics.

In order to produce that negative lift, the stabilizer must have an AOA relative to the airstream that hits it.
Because the wing generates a downwash, that airstream hits the stabilizer at several degrees coming from above.
That AOA of the stabilizer relative to the downwash should be the appropriate in order to generate the needed negative lift.

In other words: the apparent or geometric angle of the stabilizer may be misleading.

The good thing about the Vanessa device is that the plumb will always cross the actual CG, regardless of the attitude of the model; hence, extending the plumb line for two or more positions, is a sure method to locate the vertical and horizontal position of the CG.

Regards!