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Keep in mind that there is a reason to install the inner chain case with no shims and ensuring that the inner chain case does not interfere with the swingarm, and then measuring the shims required.  Once the outer primary cover is on and tightened if the shims don't stop it, the inner chain case will move towards the cradle and may again make the stator out of line.  One way to be sure is to put a spacer and nut on the center stud once the inner chain case is on and tighten to see if the inner chain case/stator move.