For best image quality, you'll want your axial collimation (getting the primary and secondary aligned with the focuser axis) to be dead on, by adjusting the secondary so that the laser hits the primary center dot, then adjusting the primary, which is what you've done.
A secondary that's slightly off-center won't affect image quality to a noticable degree, as long as you can still see the entire primary reflected. Your last paragraph has me confused - you're implying that part of your primary reflection is missing the secondary, then immediately you go on to say that you can see all the mirror clips?
If you cannot see the entire primary reflection, you are effectively reducing the aperture of the scope. If you can see the entire primary reflection, even with the secondary slightly off-center as seen through the focuser, you won't lose image quality but the field illumination might be uneven, but visually you won't notice it.
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