I'd say BS. If there was or is a knock check your fluids. Fuel issues are either a slightly poor fuel pump or the common fuel filter replacement.
As far as the doors....They are a pain but Yamaha is doing the recall to protect there liability concerns. You can take them off BUT if you get injured without doors Yamaha has your VIN number showing doors and safety issues had been corrected.
I still don't like the doors until I start flinging mud.