I had the same problem on my 2007 XTX. The knock started on at 64000 km. I went to a Yamaha dealer and the problem solved. He told me that the crank nut was loose. I believe it was the same as yours. The mechanic also replaced the piston springs, oil, oil filter, antifreeze and checked valve clearence. For about 1000 km I rode it soft, then I replaced the oil and oil filter. At 65000 km the bike felt like new. Now (66500 km) I hear a strange metallic noise from the engine when braking, like two metal sheets hitting each other. I can't figure out what it is, I have to get the bike back to the dealer...