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The fact that the collimation changes with focuser position indicates that you havent lined up the focuser axis to the optical axis.
This is step two in collimation and involves using your collimation tool to align the secondary to the centre of the mirror. With a laser this is intuitive, and using a cheshire its a matter of centering the cross hairs over the reflection of the mirror centre spot. Once this is done, the focuser axis is aligned. Then proceed to adjust the primary.
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