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Originally Posted by LaFey
...The next phase should be to center the primary mirror's reflection. But since this is done with the same three screws am I not messing what I did earlier on??...
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Yes you are, well spotted!
Collimation from badly aligned optics is an iterative process and will require you to go back and forth between steps to get it spot on.
Keep to the recommended order of steps, but don't be afraid to go back a step and repeat if required. You will quickly home in on alignment this way and in future the steps will only need to be performed once in the usual order.