HI Steve,
If you have a close look at your venting system you will see that there are two vents, each with a T to give two hoses for each vent.
Fryguy commented on this quite a while back, and I have had the same problem crossing streams. An easy experiment to prove this out: Start your bike and let it warm up to where it will idle with the choke off. Take a cup of water and insert your vent tubes into the water. It won't be long and your motor will die.
The solution, just take one vent tube from the T on each vent and run it up higher on the frame. Fryguy commented "it makes the bike into a submarine" or something very close to that.
I would however, put a bit of thought into it though. In a tip over gas will run into the vent tubes. By leaving one end lower any gas that get's into the tubes that you have run up the frame will run back down to the T, and then out the bottom tube. HOWEVER, there is the reality that gas will flow out the hose that is mounted high on the frame in a tip over. I have concerns about that gas running down on top of the motor, especially on the header pipes, which wil glow red hot if the bike is being run slowly. Any gas hitting that red hot metal and it will catch on fire, under your gas tank. Not a pretty picture to say the least. I have considered running said tubes up the back end along the frame rails on the opposite side of the exhaust.
Also, you should drain your float bowl regularly to eliminate any water that has collected there, as well as debris.
Next, go to the auto parts store and get a can of CRC dielectric grease, and some CRC lectra motive contact clearner. The grease comes in a pressurized can like cheeze wiz. Take apart ALL of your electrical connections, spray a bit of lectra motive in there and then blow out with compressed air.
Then squirt some dielectric grease in the connector, enough so that when you put it togeter it squishes out. This will help insure that any water does not get in. Clean off the excess with a rag, not the lectra motive. It will also make sure that some day when you try to take a connection apart, it will come apart.
As far as sealing the air filter area goes: I would think a piece of heater hose cut down to size and siliconed/ glued onto your frame in front of the air cleaner to make a better seal with the tank as the water wil be coming up there at a great velocity and will inturn hit the bottom of your seat and land on top of the filter with a good deal of force. The mounting area of your filter already has a ridge around it, so any water running down the back bone will stop there. Your filter is not going to just suck up water that dribbles down the back bone and gets on the foam along the bottom. The reticulated foam on the sides of the back bone should not let too much water past, even at a good splash. The area at the top of the shock mount is covered by the reticulated foam attached to your seat base. If you look up under neath, you can see the filter is exposed there as that piece of foam doesn't really seal it off well enough. Perhaps you could purchase some of this foam and make a better seal there so any water splashing up the side of your boots will not go right onto the filter. I regularly clean that piece of foam and even with a good spray of water from the hose, it doesn't go far when sprayed through that foam.
Hope this helps, and good luck!
, the foam is a much better idea!!
