From the top of my head its just under 3 litres from empty that yamaha recommend with a filter change, if you know how much you put in, just drain the right amount out, if its I little over you should be ok as its a dry sump engine, so over on dipstick is only in the holding tank so to speak, if you got a clean container just drain the lot and start again,

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K+N filter, snorkel removed, homemade kev mod (with his blessing), co raised,
Pipeworx cans, r1 led back light, under tray removed, small indicators, handguards, cnc short levers,