so to the op:

you had to of parked where your bike wasnt really leaning on the stand or in gravel of the grass to have your bike fall over from a heavy rain storm. that or some outstanding winds. i would think that someone pushed it over etc.

but as far as maintaince to the bike, id pull the plugs and get a turkey baster in there and suck out the oil on the piston. if theres a little left that wont be a big deal as it will jsut burn off and may foul out the plug. this isnt like hydrolocking your motor b/c you never got water sucked up into the engine while running.

i still dont get how the bike just fell over from a heavy rain storm. keep a watch next time you park and look at getting a kickstand pad.