The backstory is that I tried to run with pod filters, and the bike ran beautifully until we got to operating temperature and then it was all over the place. (Please be kind because right here, and right now, I really don't need tirade of "I told you so's" that could come).
I didn't once say "I told you so Peter" when you dropped in yesterday, and i am certainly not going to now. It is perfectly possible to build a custom induction system, that will leave your airhead every bit as tractable as standard and will not suck in water.
The first thing is the intake induction tubes which form part of a "tuned length" system, it's not hard to measure the BMW ones and the appropriate sized tubing is available in both alloy and structural resin. Small problem though, the ends of the tubes will be about where your ankles want to be, and you haven't yet fitted an air-cleaner. The secret is of course to bend the intake tubes upwards (you could bend them downwards of course, but then they would pick up road grime and heat from the exhaust.
Now that your "velocity stacks" are all nicely curved in order to get the right length in a confined space you need to organize some air filtration.
You could of course fit the accused pod "filters" (in fact they do bugger all filtering but K&N have a very effective marketing arm) but you would the have a small problem in wet weather, or if you need to cross a flooded gutter, or gasp, a small creek crossing.
So you get to build a waterproof housing to contain your filtering system and keep the elements at bay.
And when you finish, your bike will run perfectly. now along the way you will probably design the air-filter carrier so that it is as large as possible, and if you are really clever, it will be cunningly made so that a stock, readily available filter slips right in.
As you finish your design and start cutting metal (or plastic) you could give some thought to a system to allow the engine itself to dispose of nasty crank case gasses and the small amount of oil that comes with them.
The last step will be to use a good dyno and give the air intakes into your air filtration system a good tune up as there is horsepower and economy both to had by careful design in this area.
And, when you have finished all that, it will probably look like the first picture below.
There are alternatives like the one in the 2nd photo, for an alleged gain of a whole 2 horsepower (on an R80) you get one of those egregious waste of money pretend filters from K&N and guaranteed induction howl to keep you awake on the bike.
http://www.bmwr65.org/htdocs/yabb2.612files/yabbfiles//Templates/Forum/default/grin.gifP.S I hope you have two pots running by now.