Could they be meeting at the top of the suspension travel? Look for "tell" marks on the kickstand, if the swingarm is rubbed then so is the kickstand or what ever is rubbbing the swingarm. If you can't find the tell mark I would cover the swingarm rub mark in grese or vasaline and try to rub some off on the kickstand while riding. That should tell you where it is making contact.
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