Dry out the spark plug wells before you fire up the bike.
Running the engine with a lot of water in there really
p---es off the gremlins.
Other than that, a little rain wouldn't hurt anything.
In saying that, I'm assuming the exhaust pipes will be facing rearward while in transit...
If for some reason the pipes were pointed forward,
a very heavy rain could have the potential to hydraulic it's way into the engine.
Not likely, but some tape or a couplea rags stuffed into the pipes would cure that scenario.
I prefer to move a bike with the tranny in neutral, so that if it moves a little, it isn't banging the gears or engine innards around.