Not that I'll make any changes to my bike, but I had to do some 'fording' on my way home from the most current trip. In fact, I waited at one wash for about an hour till it went down enough that I was comfortable crossing. Up to the axles in a couple places. While I was waiting I saw several idiots cross it. Two hit it at 30 plus mph and I actually was afraid but they both skidded the other direction.
So. My brother just got a Subaru Outback Wilderness. He plans to drive it to his place in Panama. I'm sure he's thought of the air intake but I'll remind him of the need for the diffs. Costa Rica and Panama (he owns property in each) are very wet environments with water crossings the norm for rural roads.
It's a cool car that has the same ground clearance as the stock Jeep Wrangler and a lot better skid plate system. Subaru's 4wd is solid.
I've serviced submerged equipment. Depending on circumstances it's never pretty. I did buy a tractor that I knew had been submerged sitting in a flood. It was never started after and I tore it down and cleaned rigorously. I got a cheap tractor out of the deal...
RE: Breathing under water