Something I haven't seen mentioned, but could be a factor, is damage to the exhaust.
I have a ninja 250 and 500 that have both been knocked over. When this happens, it seems to have a tendency to Ben the mufflers inward, fairly significantly in the case of the 500. On the 250, it actually brought the muffler into contact with the swingarm. Could this be the case here, where the OP's exhaust was bent inward enough to cause interference?
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