TiPwEiGhT,
If your engineers are equiped to do it, then you could fly with an accelerometer stuck to the fuselage. This could be inside the cockpit, near where you felt the vibration, to avoid any complications. The idea is to convert the signal into a frequency plot, to understand the cause. It works because engine, main rotor and tail rotor are geared to rotate at different frequencies.
You haven't mentioned tail rotor by the way - any constraints on flapping? Is drive shaft running out of balance?
For general vibration work, with variable RPM, a Campbell diagram is a great way to pinpoint the source of a vibration
