All LensAlgin test shots should be done at full aperture (f1.4, f2, f2.8, etc) of the lens. The only time to check at a smaller physical aperture (larger number) would be if the lens exhibits focus shift where, in fact, the Focus point will be different wide open as opposed to 1 or 2 stops down. This usually happens on fast primes (when it happens). After setting an AF Adjustment, you should also test at 1 and 2 stops down just to see that the lens does not exhibit focus shift.
Note: Alignment of LensAlign to the camera should be done at f8 so the greater DOF makes setup and parallel alignment easier.