Did you get any resolution to the post-soaking misbehaviour in the end? Reading through this thread for the first time (sorry, a bit belated) a thought occurred to me - a number of us have Yamaha WR250Fs for green-laning, and Yamaha made an inexplicable engineering decision to route the carb breather hoses down beneath the engine, one of which is under vacuum from the carb and draws up water whenever you go through water in excess of about 25cm (10") in depth and promptly kills the engine... 25cm of water... and these are off-roaders *rolls eyes* Fortunately we have a fine work-around that involves re-routing the hoses and keeping them above the engine.
I may be wrong, but your bike's symptoms and the pre-cursor event sound just like water being drawn in by a breather hose. Apologies for the rather rambling anecdote....
