Remember the old carburetor four cyl bikes, when the carbs were out of sinc the clutch would sometimes rattle so much you were scared to ride it for fear that there was something "wrong" with the engine internals...?!! Personally I would say you are looking at a fuel problem, petrol is hyroscopic which means it attracts water particularly at sea level, if that bike stood for a long time like you say with about half a tank of fuel then you may have ingested some water into the system which may have damaged something like the injectors. Maybe you will be lucky with a full flush out, do yourself a favour and throw whatever is left in the tank away too.....