I am using Motul 5100 with API Standards: API SG/SH/SJ/SL/SM (http://www.motul.com/gb/en/products/oils-lubricants/5100-4t-15w50--2) is it possible that caused problems in the first place?
That's fine, 10W40 is what most of us are using so you're already using a slightly thicker oil.
It looks more and more like the selector forks are the cause of your problem.
I doubt it is fine. Motul 5100 bought in Serbia is pure rubbish. I'd avoid it. Motul 7100, Bel Ray, or evene Silkolene, but do avoid 5100.
I also get rattle sound when revs are not right, not matched. 1st to 2nd. It has been like that for some 40,000+ kms, since I bought the bike. Doesn't get any better or worse. When doing clutchless upshifts I have no problems, as well as when getting the revs right. Now, having read all this, I'm not sure if I have a problem, or is it just normal FZS behaviour. Deefer?
Edit: coming from 2nd to 1st also does rattling when revs are not matched, usually when going 30km/h+ in neutral, with engine idling at 1300 rpm and trying to put it into 1st. Slowing down below 20 km/h, or blipping the throttle, or just being slow and patient on the lever all do the job. But like I said, it has been like this ever since I got the bike (some 30,000 km, now it has under 70,000 kms and has been the same - not better, not worse).