Didn't the BMW military sidecar rigs have the air filter inside the fuel tank with the air intake coming out of the top of the tank, I remember the top filter cover looking like a helmet????? A person could use a can big enough to hold the round BMW filters and add water drain holes outside of the filter area to drain the water out the bottom. You would lose some fuel volume but you would have the area were the airfilter use to sit to make an additional fuel tank or mount the battery in that position and then build the extra fuel tank were the battery use to sit. This would also be a good area to run the trans and rear end vents to keep them out of the water.
Seems like BMW had a good idea 60 years ago.