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I have a bad vibration around 3000 rpm to 3500 rpm. The problem is still there even if you bring engine to the same rpm's while in neutral or with the clutch released. The problem get worse with the ac on but the rpm is still the same. it will get worse as engine heat increases .
The good part is that you have narrowed it down to something rotating, the bad part is what?
If I were you I would take the serpentine belt off of your car and start it. You can run it safely like this for 1-2 minutes. Just be sure to monitor your coolant oil temperatures. Just do this long enough so that you can bring the rev's up to 3000-3500 a couple times to see if the vibration is still there.
If it is, then it is the engine or tranny. If it is not there, it is one of the accessories. You said it is worse with the AC on? Could your AC compressor clutch bearings be biting the dust?
Sounds like a harmonic dampener to me. Take your belt off and if you still feel vibrations I'd start there. It may also be your flywheel but hopefully you're aware of what condition it's in through maintenance records.