NavList:

Hello George

You wrote
I think the problem I am having is squaring/aligning with the optical path. As-is you can not level the unit, the exterior case appears to be protective and not designed to sit on a flat surface. There are three screw attachment points found around the objective lens. I am assuming these are inline with the system.

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You will need to create a master reference in order to properly calibrate your autocollimator.  This master reference will consist of a mirror with three legs.  The three legs will attach at those three screw attachment points you mentioned.  The mirror plane relative to plane formed by those attachment points should be with zero (or minimal) pitch and yaw.  Thus the measurement path will possess the qualities of a 'zero reference'.  This most likely will require a machine shop. ***

Using such a reference will permit you to adjust the adjustable mirror and the overall optical path.  With a reference,  finding the twist in the optical path will be simplified.  Depending on the sensitivity of the instrument, lightly pressing on each of the optical components will disclose which contributes to the askew'd nature. 

In summary, the overall calibration of the autocollimator involves more than just skew.  Since your goal is calibration, something that the manufacturer can't or won't do, then proceed in that direction yourself.  Twist or skew is just one component!

Brad

*** an open ring in which to mount a front surface mirror, the face of which to be parallel to the plane of the attachment points.  Place mirror into open ring, reflective surface onto that parallel face.  This is fairly simple, merely requiring two parallel planes.