I really don't know of a sure fire way of keeping water out for sure unless you snorkel.
But how often do you go driving through water that comes to the roof of the cab??
I have made baffles to keep water out of other things before.... I am not going to say for what application for this is a family site, but it works. It really cuts down the water intake.
Do you have an electric pump for beds or anything?? I had a rig setup before that drew air through the top got filtered by water, and the baffles kept the water from entering the pump....
It worked really well too. there was a clear tube that ran from the output to the user, and I never found any water droplets out of the many times i had used it.
The biggest problem I see with using baffles for the intake on your engine is the fact that baffles mess up your air flow. The air should move in unrestricted, and crap kept out of it's way.
But I geuss if you are going to chop your thingy shorter, and point it towards your distributor, then maybe you could jerry-rig something up before you molest your thingy. That way if the baffle doesn't work, then atleast you know.....