bullwinkle

I have 9 bikes of different manufactures and all of them have these issues with 'clunks' and shifting to a degree (some worse than others).  Sometimes: upshifting to 2nd at a stop prior to engaging 1st gear, eases the situation. 

My 2017 FJ09 has it.  AND it sounds exactly like my wife's 2016 FZ09's; so, presume that whine is normal.  

I've pressured washed my factory bags with a garden hose and never noticed any water inside afterwards; but if really concerned, fall back on the old fashion/time tested remedy of plastic trash bags for piece of mind.