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your entire alignment is off. you need to get the bike perfectly perpendicular to the ground. Verify this with an angle measuring device on the front caliper. Get the rear wheel off the ground and check the rear rotor. by adjusting the width of the top motor mount you can adjust the bikes alignment so that both discs are within 1 deg of each other.
If you have the service manual. Pages 2-28 and 2-29 describe the procedure for getting the vehical alignment set right. Also check the swing arm berrings, and check to make sure the swingarm is not bent or cracked.
It must have progressed over time since I have never had the rear wheel off the bike.
Also, the only things I have ever done is install a new after-market stabilizer link (the one on top of the engine, the new one has rubber bushings and took care of a lot of the vibes).
After I installed the new stabilizer link I did the "engine alignment" procedure in the shop manual. All that entailed was loosening the stabilizer link and engine mounts and running the engine for a minute to align it. Then you just tighten everything up.
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