That motor has had water sitting in it for a while as it had corroded some sections in the bottom of the casing under the clutch, the lowest point in the cover. Don't want to scare you mate, but it may be worthwhile splitting the cases to check on the gears & bearings, if your up to that sort of thing.
It should be a bit easier to flush out with the clutch cover off by laying the bike on either side to fill & drain.
Completly drowned my KX 125 in a creek crossing once, unbeknown at the time filling the gearbox full of water.
I found out after the event when draining. I filled with fresh oil, warmed it up to mix everthing up & drained it striaght away, Same again after the first short ride & it was fine after that.
