So you made the gears yourself. That’s very impressive. Nice work! Regardless of the frequency, my point is that highest frequency shown is at the rotational frequency of the motor.
From what I know about helicopter dynamics here are the sources of vibrations in the non-rotating frame. Vibrations from the rotors due to oscillatory air loads transform into the non-rotating frame in the vertical axis at the number of blades on the rotor. For example two bladed rotor would have vibrations come through at two times the rotor rotational frequency. In the horizontal plane, rotor vibrations would come through in the non-rotating frame at 1 plus and 1 minus the rotor rotational frequency times the number of blades. For example, 4 bladed rotor system would have vibrations in the horizontal plane at 3 and 5 times the rotor rotational frequency. The other big vibration driver in the fixed frame would be the lead lag modes of the rotor. Based on your frequency of 2250 RPM, your lead lag frequencies are 1376 and 3124 RPM in the non-rotating frame.
Any of these frequencies could couple with the aircraft structure. So placement of the pixhawk could impact the vibrations it would feel.
If the vibrations come through at the same magnitude regardless of the head speed then it is more a drive train or rotor vibration. If the vibration magnitude seems to peak at some head speed and subside at other head speeds then the it could be the rotor coupling with the airframe structure. Unfortunately there is no smoking gun that points to the source of the vibration.
I’m sorry I could not be more helpful.