My gear box also makes a little noise from 2nd to 3rd, but it's consider normal.
Is the noise constant in every gear?
This could sound stupid but is also a reason for vibration noise. Do you have a protection engine bar? Is it the same has the Givi that has a union in the middle of it?
With the bike side stand and neutral, accelerate and if the noise comes up, old your protection bar, if the noise stops, than your problem is vibration in the protection bars. You can fix with rubber or something.