Have you checked the gear box oil?

My old aprilia would whine if it burnt a little oil. Solved buy a simple top up.

I have disconnected my balance shaft on my MK3, I just replaced the gear with a brass spacer. more vibes when cold but for what I use my mk3 for I can't really notice the difference when it is warm and it does make the engine a big quicker on throttle response but less engine breaking

There is no noise at all at tickover only when you increase the revs?