Wow, it's been a while, but the problem is finally solved.
Here's the story:
I took the bike to a" friend of a friend", who's a retired mechanic but still does odd jobs from time to time. After a day, he diagnosed loose oil pump drive chain. He installed new one, and claimed the rattle to be gone (yay!). Spoiler alert- it wasn't (boo!). For future reference- that chain is not tensioned and looks super loose from the factory. After that fiasco he threw the towel and refused to investigate further.In the meantime I was in a process of buying new house, so unfortunately didn't have time, money, or willpower to deal with my poor bike.
After dust finally settled down it was time for second round. I took her to different garage, and then they discovered it was gearbox problem
Now, could sell it and make it someone's else problem, but I'd rather had a bike I knew was 100% solid. It took a while to strip the engine, but eventually we found what the issue was. One of selector forks was slightly bent, rubbing against 4th gear wheel and it was just slightly touching its neighbour- hence the rattle. Yamaha quoted cool £560 just for the wheel
, but I managed to get used gearbox from ebay for just £150. After replacing damaged parts, flushing entire engine in case some debris made it through the filter, new back tyre and fresh MOT, the bike is back on the road!
The culprit[smg id=3590]
Damaged wheel[smg id=3591]