I have a 2013 / 250 factory bike and plagued with exact problem, rattle under load on hill climb (not noticed the smoke part). I have already changed to the 48 pilot, needle and splatshop washer on the second bottom position and changed to thinner needle (ggj from ggh STD?) but still the same problem. I was given a spare main jet with the bike (125) which I have not tried as yet. Not sure what size the STD main is.
Crankcase oil level not moved at any time but changed very regularly. I was brought up on two strokes and love the factory but have to admit I am for the first time tempted to try a 4RT because of this! Tried every thing other than the 3,0 slide and would not be surprised now to find Mains problem.. Few weeks ago bike started choking on idle like fuel was switched off which was transiently mitigated by use of the choke... not happy!