With the XLK autocollimator, you should be able to achieve aligned images via both pupils. Secondary offset or having an off-center spot should not impact the ability to achieve aligned images via both pupils.
Try to re-iterate. Align the images via the offset pupil by only adjusting the secondary then align the images via the central pupil buy only adjusting the primary mirror.
http://www.youtube.com/watch?v=Vj12cx3tnsM
Jason
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