Thanks gents. There is no misalignment in the optical train that I can detect with my laser equipment. I suspect that when I bonded in the front frame member (which was done after the alignment test) that the frame might be just that little bit out of position. That is not a big deal over a 1250mm focal length and where the vanes are adjustable. To Alex's question, the four vane spider is not set with a vane parallel or perpendicular to the focuser. I am familiar with offset and considered that when I first noticed the different vane lengths. The secondary may well be perfectly optically centred as the frame openings are larger than the mirror diametre, and if the placement of the front frame was slightly out alignment it may have no effect. Photo attached. More photos in my Imaging Newt build thread.
Note that the photo is not optically centred, just a view down the tube, hence any appearance (or assumption) that the secondary might not be centred on the holder are not correct. The secondary minor axis is 63mm but when viewed down, most of what you see is the top of the secondary holder which is just 52mm in diametre.
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