It does not really matter if the focuser is exactly square to the tube. The focuser axis will define your optical axis when you collimate, wherever the focuser axis is pointing. The tilt and rotate adjustments of the secondary will align it to the focuser axis. Having said that I did spend a bit of time adjusting my focuser because I found it helped in minimising the adjustments needed to initially get the secondary centred in the sight tube. If you really want to delve into collimation I found Vic Menard's booklet "New Perspectives on Newtonian Collimation" very useful and a wealth of information.
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