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Check your engine mounts.
I've never noticed a vibration on my Electra Glide other than the shaking at idle.
I hear oil can destroy the lower front mount if you let the oil run on it when changing the filter.
2500-3000 is lugging the motor for other than cruising. You are hammering the bottom end at those RPMs with hard acceleration.
I usually shift before 3000. Peak torque is around 2800. My bike does not "lug" unless I roll on at below 2000. FTR, I have over 100,000 miles on my motor and it still runs strong.
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