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Check the bolt connecting the bottom front of the engine to the frame. I had an '01 Ultra and checked mine and the bolt was about ready to fall out. I do not recall the torque spec. A dealer wouldn't charge much to check your motor mounts if you don't have a service manual.
Got it back together last night, no vibration. Other than the socket that I found between the engine & the frame, all I did was readjust the primary chain to the 5/8" cold.
Always have to look at everything....I was having the Vibe/shutter at 3k too, unfortunately I had just put in Sta-BO bushings found my rear fork caps loose and reworked the exhaust mount to the trans (never ever did it clamp and now it does). After all of that the shutter became very noticeable so as one can imagine I was unsure at which fix caused the "new" vibration.
I was very worried about run-out and/or the motor mount so I checked both. What it turned out to be was the front exhaust tube hitting the brake pedal. I ground a little out of the pedal and the shutter is gone. I had always had a vibration but it was totally amplified and I felt it through the pegs, boards and seat.
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